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Atasoy M, Cetecioglu Z. Bioaugmentation as a strategy for tailor-made volatile fatty acid production. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 295:113093. [PMID: 34167052 DOI: 10.1016/j.jenvman.2021.113093] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
This study aimed to develop a novel strategy for tailor-made volatile fatty acid (VFA) composition. For this purpose, the mixed microbial culture was bioaugmented by Propionibacterium acidipropionici. Anaerobic sequencing batch reactors were operated with cheese wastewater under alkali pH. While the maximum propionic acid production almost four times increased (3779 ± 201 mgCODeq propionic acid/L in the bioaugmented reactor and 942 ± 172 mgCODeq propionic acid/L in the control reactor), there was no significant difference in VFA composition. The gene copy number of P.acidipropionici increased 20 times after the bioaugmentation. Furthermore, the gene copy number of P.acidipropionici was positively correlated with total VFA and isovaleric acid concentration. The relative abundance of family Flavobacteriaceae increased in the bioaugmented reactor, which might be caused by the syntrophic relation between Flavobacteriaceae and P. acidipropionici. The cycle analysis results showed that the shorter cycle (6h) could ensure the same efficiency.
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Affiliation(s)
- Merve Atasoy
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE, 100 44, Sweden.
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE, 100 44, Sweden
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2
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Chen J, Harstad OM, McAllister T, Dörsch P, Holo H. Propionic acid bacteria enhance ruminal feed degradation and reduce methane production in vitro. ACTA AGR SCAND A-AN 2020. [DOI: 10.1080/09064702.2020.1737215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jikun Chen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Odd Magne Harstad
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Tim McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Canada
| | - Peter Dörsch
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Helge Holo
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Tine SA, Oslo, Norway
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3
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Rinttilä T, Ülle K, Apajalahti J, Timmons R, Moran CA. Design and validation of a real-time PCR technique for assessing the level of inclusion of fungus- and yeast-based additives in feeds. J Microbiol Methods 2020; 171:105867. [PMID: 32061906 DOI: 10.1016/j.mimet.2020.105867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 11/30/2022]
Abstract
A reliable method for quantification of non-viable microbe-based nutritional and zootechnical additives introduced into feed is essential in order to ensure regulatory compliance, feed safety and product authenticity in industrial applications. In the present work, we developed a novel real-time quantitative polymerase chain reaction (qPCR) -based analysis protocol for monitoring two microbial additives in feed matrices. To evaluate the applicability of the method, pelleted wheat- and maize-based broiler chicken diets containing a non-viable phytase-producing strain of Aspergillus niger produced in solid state fermentation (150 or 300 g/t) and a non-viable selenium-enriched Saccharomyces cerevisiae (100 or 200 g/t) as model feed ingredients, were manufactured and subjected to analysis. Power analysis of the qPCR results indicated that 2 to 6 replicate feed samples were required to distinguish the product doses applied, which confirms that the microbial DNA was efficiently recovered and that potential PCR inhibitors present in the feed material were successfully removed in DNA extraction. The analysis concept described here was shown to be an accurate and sensitive tool for monitoring the inclusion levels of non-viable, unculturable microbial supplements in animal diets.
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Affiliation(s)
- Teemu Rinttilä
- Alimetrics Research Ltd., Koskelontie 19B, FI-02920 Espoo, Finland.
| | - Kir Ülle
- Alimetrics Research Ltd., Koskelontie 19B, FI-02920 Espoo, Finland
| | - Juha Apajalahti
- Alimetrics Research Ltd., Koskelontie 19B, FI-02920 Espoo, Finland
| | - Rebecca Timmons
- Alltech Inc., 3031 Catnip Hill Road, Nicholasville, KY 40356, USA
| | - Colm A Moran
- Alltech SARL, Rue Charles Amand, 14500 Vire, France
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4
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Strain-Specific Quantification of Native Probiotic Bacillus spp. and Their Effect on Liver Function and Gut Microflora of Experimental Rats. Probiotics Antimicrob Proteins 2018; 11:478-492. [PMID: 29512027 DOI: 10.1007/s12602-018-9391-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Safety and efficacy was investigated for two candidate probiotic B. flexus MCC2427 and B. licheniformis MCC2512 via in vivo studies on albino Wistar rats. In acute toxicity assay, rats were fed with single dose of 1010 cfu mL-1 of probiotics. The follow-up studies for next 14 days did not reveal any toxicity-related criteria indicating the non-toxicity nature of probiotics. In 90-day repeated dosage studies, the cultures were administered in three doses (106, 107, 108 cfu mL-1). Results showed no overt toxic effect and no drastic treatment-related changes pertaining to histopathology of vital organs. DNA fingerprinting indicated the lack of bacterial translocation. Superoxide dismutase and catalase activity indicated their antioxidant potential. Reduced serum cholesterol with improved HDL-cholesterol specified the cholesterol-reducing ability of the cultures, which was also apparent with increased excretion of cholic acid in feces. Both probiotic cultures positively altered the gut microbial environment, retained lactic acid bacterial effect, and simultaneously reduced pathogenic strains. A sensitive and rapid tool was developed using strain-specific qPCR primers, which facilitated appropriate estimation of test culture in feces. The data strongly advocate the safety of tested probiotics at levels used in the study.
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Azad E, Narvaez N, Derakhshani H, Allazeh AY, Wang Y, McAllister TA, Khafipour E. Effect of Propionibacterium acidipropionici P169 on the rumen and faecal microbiota of beef cattle fed a maize-based finishing diet. Benef Microbes 2017; 8:785-799. [PMID: 28856906 DOI: 10.3920/bm2016.0145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Direct fed microbial supplementation with lactic acid utilising bacteria (i.e. Propionibacterium acidipropionici P169) has been shown to alleviate the severity of subacute ruminal acidosis in high-grain fed beef cattle. This study was carried out to explore the impact of P169 supplementation on modulating rumen and hindgut microbiota of high-grain fed steers. Seven ruminally-canulated high-grain fed steers were randomly assigned to two treatment groups: control diet (n=3) and the same diet supplemented with P169 added at a rate of 1×1011 cfu/head/d (n=4). Samples were collected every 28 days for a 101 d period (5 time points) and subjected to qPCR quantification of P169 and high-throughput sequencing of bacterial V4 16S rRNA genes. Ruminal abundance of P169 was maintained at elevated levels (P=0.03) both in liquid and solid fractions post supplementation. Concomitant with decreased proportion of amylolytic (such as Prevotella) and key lactate-utilisers (such as Veillonellaceae and Megasphaera), the proportions of cellulolytic bacterial lineages (such as Ruminococcaceae, Lachnospiraceae, Clostridiaceae, and Christensenellaceae) were enriched in the rumen microbiota of P169-supplemented steers. These, coupled with elevated molar proportions of branched-chain fatty acids and increased concentration of ammonia in the rumen content of P169-supplemented steers, indicated an improved state of fibrolytic and proteolytic activity in response to P169 supplementation. Further, exploring the hindgut microbiota of P169-supplemented steers revealed enrichment of major amylolytic bacterial lineages, such as Prevotella, Blautia, and Succinivibrionaceae, which might be indicative of an increased availability of carbohydrates in the hindgut ecosystem following P169 supplementation. Collectively, the present study provides insights into the microbiota dynamics that underlie the P169-associated shifts in the rumen fermentation profile of high-grain fed steers.
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Affiliation(s)
- E Azad
- 1 Department of Animal Science, University of Manitoba, 12 Dafoe road, Winnipeg, MB R3T 2N2, Canada
| | - N Narvaez
- 2 Agriculture and Agri-Food Canada, Lethbridge Research Center, 5403 1 Ave S, Lethbridge, AB T1J 4P4, Canada
| | - H Derakhshani
- 1 Department of Animal Science, University of Manitoba, 12 Dafoe road, Winnipeg, MB R3T 2N2, Canada
| | - A Y Allazeh
- 2 Agriculture and Agri-Food Canada, Lethbridge Research Center, 5403 1 Ave S, Lethbridge, AB T1J 4P4, Canada.,4 Department of Clinical Nutrition, College of Applied Medical Sciences, P.O. Box 2440, University of Hail, Saudi Arabia
| | - Y Wang
- 2 Agriculture and Agri-Food Canada, Lethbridge Research Center, 5403 1 Ave S, Lethbridge, AB T1J 4P4, Canada
| | - T A McAllister
- 1 Department of Animal Science, University of Manitoba, 12 Dafoe road, Winnipeg, MB R3T 2N2, Canada.,2 Agriculture and Agri-Food Canada, Lethbridge Research Center, 5403 1 Ave S, Lethbridge, AB T1J 4P4, Canada
| | - E Khafipour
- 1 Department of Animal Science, University of Manitoba, 12 Dafoe road, Winnipeg, MB R3T 2N2, Canada.,3 Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
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A "Ct contrast"-based strain-specific real-time quantitative PCR system for Lactobacilllus paracasei subsp. paracasei NTU 101. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 51:535-544. [PMID: 28693925 DOI: 10.1016/j.jmii.2017.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 06/18/2016] [Accepted: 05/24/2017] [Indexed: 11/23/2022]
Abstract
BACKGROUND/PURPOSES Routine cell number determination for specific Lactobacillus strain by cultivation requires at least 4-7 days. Thus rapid and specific cell number determine methods such as strain-specific quantitative PCR (qPCR) are valuable. However, qPCR method is vulnerable to difficult PCR target such as dimer/secondary structure forming sequence. METHODS In this study, a two-component, "Ct contrast" approach was applied to strain-specific qPCR system following the development of Lactobacillus paracasei subsp. paracasei NTU 101 (NTU 101) strain-specific PCR with random amplification of polymorphic DNA (RAPD)-derived strain-specific sequences. RESULTS The quantitative range of the NTU 101 strain-specific qPCR system was 3.0 × 101 to 3.0 × 105 copies for pure cultures, and 3.0 × 102 to 3.0 × 105 copies for multi-strain or unknown food samples. The results of spike in test and real sample testing suggested that non-specific weak background signals did not compromise test specificity, and demonstrated the potential of the NTU 101 strain-specific qPCR system in food samples. CONCLUSION The two-component, "Ct contrast" approach is useful for qPCR discrimination when no ideal PCR target is available or the variance of the target site is unpredictable. The Ct contrast approach might provide a simple and robust solution for other challenging qPCR targets.
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Scholz CFP, Kilian M. The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov. Int J Syst Evol Microbiol 2016; 66:4422-4432. [DOI: 10.1099/ijsem.0.001367] [Citation(s) in RCA: 329] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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8
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Fibi S, Klose V, Mohnl M, Weber B, Haslberger AG, Sattler VA. Suppression subtractive hybridisation and real-time PCR for strain-specific quantification of the probiotic Bifidobacterium animalis BAN in broiler feed. J Microbiol Methods 2016; 123:94-100. [PMID: 26883620 DOI: 10.1016/j.mimet.2016.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/10/2016] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
Abstract
To ensure quality management during the production processes of probiotics and for efficacy testing in vivo, accurate tools are needed for the identification and quantification of probiotic strains. In this study, a strain-specific qPCR assay based on Suppression Subtractive Hybridisation (SSH) for identifying unique sequences, was developed to quantify the strain Bifidobacterium animalis BAN in broiler feed. Seventy potential BAN specific sequences were obtained after SSH of the BAN genome, with a pool of closely related strain genomes and subsequent differential screening by dot blot hybridisation. Primers were designed for 30 sequences which showed no match with any sequence database entry, using BLAST and FASTA. Primer specificity was assessed by qPCR using 45 non-target strains and species in a stepwise approach. Primer T39_S2 was the only primer pair without any unspecific binding properties and it showed a PCR efficiency of 80% with a Cq value of 17.32 for 20 ng BAN DNA. Optimised feed-matrix dependent calibration curve for the quantification of BAN was generated, ranging from 6.28 × 10(3)cfu g(-1) to 1.61 × 10(6)cfu g(-1). Limit of detection of the qPCR assay was 2 × 10(1)cfu g(-1) BAN. Applicability of the strain-specific qPCR assay was confirmed in a spiking experiment which added BAN to the feed in two concentrations, 2 × 10(6)cfu g(-1) and 2 × 10(4)cfu g(-1). Results showed BAN mean recovery rates in feed of 1.44 × 10(6) ± 4.39 × 10(5)cfu g(-1) and 1.59 × 10(4) ± 1.69 × 10(4)cfu g(-1), respectively. The presented BAN-specific qPCR assay can be applied in animal feeding trials, in order to control the correct inclusion rates of the probiotic to the feed, and it could further be adapted, to monitor the uptake of the probiotic into the gastrointestinal tract of broiler chickens.
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Affiliation(s)
- Silvia Fibi
- BIOMIN Research Center, Technopark 1A, 3430 Tulln, Austria.
| | - Viviana Klose
- BIOMIN Research Center, Technopark 1A, 3430 Tulln, Austria
| | - Michaela Mohnl
- BIOMIN Research Center, Technopark 1A, 3430 Tulln, Austria
| | - Barbara Weber
- BIOMIN Research Center, Technopark 1A, 3430 Tulln, Austria
| | - Alexander G Haslberger
- University of Vienna, Department of Nutritional Sciences, Althanstraße 14, 1090 Vienna, Austria
| | - Verity Ann Sattler
- University of Vienna, Department of Nutritional Sciences, Althanstraße 14, 1090 Vienna, Austria
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9
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Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions. Appl Microbiol Biotechnol 2015; 99:5801-15. [DOI: 10.1007/s00253-015-6739-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/23/2015] [Accepted: 05/29/2015] [Indexed: 12/11/2022]
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10
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Abstract
Since health benefits conferred by probiotics are strain-specific, identification to the strain level is mandatory to allow the monitoring of the presence and the abundance of specific probiotic in a product or in a gastrointestinal tract. Compared to standard plate counts, the reduced duration of the assays and higher specificity makes PCR-based methods (standard PCR and quantitative PCR) very appropriate for detection or quantification of probiotics. Development of strain-specific assay consists of 4 main stages: (1) strain-specific marker identification; (2) construction of potential strain-specific primers; (3) validation on DNA from pure cultures of target and related strains; and (4) validation on spiked samples. The most important and also the most challenging step is the identification of strain-specific sequences, which can be subsequently targeted by specific primers or probes. Such regions can be identified on sequences derived from 16S-23S internally transcribed spacers, randomly amplified polymorphic DNA, representational difference analysis and suppression subtractive hybridisation. Already known phenotypic or genotypic characteristics of the target strain can also be used to develop the strain-specific assay. However, the initial stage of strain-specific assay development can be replaced by comparative genomics analysis of target genome with related genomes in public databases. Advances in whole genome sequencing (WGS) have resulted in a cost reduction for bacterial genome sequencing and consequently have made this approach available to most laboratories. In the present paper I reviewed the available literature on PCR and qPCR assays developed for detection of a specific probiotic strain and discussed future WGS and comparative genomics-based approaches.
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Affiliation(s)
- P Treven
- 1 University of Ljubljana, Biotechnical Faculty, Institute of Dairy Science and Probiotics, Groblje 3, 1230 Domžale, Slovenia
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Alazzeh AY, Smith AH, Beauchemin KA, Meale SJ, McAllister TA. Supplementing Propionibacterium acidipropioniciP169 does not affect methane production or volatile fatty acid profiles of different diets in in vitrorumen cultures from heifers. ACTA AGR SCAND A-AN 2014. [DOI: 10.1080/09064702.2014.988746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Vyas D, McGeough EJ, McGinn SM, McAllister TA, Beauchemin KA. Effect of Propionibacterium spp. on ruminal fermentation, nutrient digestibility, and methane emissions in beef heifers fed a high-forage diet1. J Anim Sci 2014; 92:2192-201. [DOI: 10.2527/jas.2013-7492] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- D. Vyas
- Lethbridge Research Center, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - E. J. McGeough
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - S. M. McGinn
- Lethbridge Research Center, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - T. A. McAllister
- Lethbridge Research Center, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - K. A. Beauchemin
- Lethbridge Research Center, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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Sattler VA, Mohnl M, Klose V. Development of a strain-specific real-time PCR assay for enumeration of a probiotic Lactobacillus reuteri in chicken feed and intestine. PLoS One 2014; 9:e90208. [PMID: 24587284 PMCID: PMC3937354 DOI: 10.1371/journal.pone.0090208] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/28/2014] [Indexed: 11/24/2022] Open
Abstract
A strain-specific real-time PCR assay was developed for quantification of a probiotic Lactobacillus reuteri (DSM 16350) in poultry feed and intestine. The specific primers were designed based on a genomic sequence of the strain derived from suppression subtractive hybridization with the type strain L. reuteri DSM 20016. Specificity was tested using a set of non-target strains from several sources. Applicability of the real-time PCR assay was evaluated in a controlled broiler feeding trial by using standard curves specific for feed and intestinal matrices. The amount of the probiotic L. reuteri was determined in feed from three feeding phases and in intestinal samples of the jejunum, ileum, and caecum of three, 14, and 39 day old birds. L. reuteri DSM 16350 cells were enumerated in all feeds supplemented with the probiotic close to the inclusion rate of 7.0×103 cfu/g, however, were not detected in L. reuteri DSM 16350 free feed. In three day old birds L. reuteri DSM 16350 was only detected in intestinal samples from probiotic fed animals ranging from 8.2±7.8×105 cfu/g in the jejunum, 1.0±1.1×107 cfu/g in the ileum, and 2.5±5.7×105 cfu/g in the caecum. Similar results were obtained for intestinal samples of older birds (14 and 39 days). With increasing age of the animals the amount of L. reuteri signals in the control animals, however, also increased, indicating the appearance of highly similar bacterial genomes in the gut microbiota. The L. reuteri DSM 16350 qPCR assay could be used in future for feeding trials to assure the accurate inclusion of the supplement to the feed and to monitor it's uptake into the GIT of young chicken.
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Affiliation(s)
- Verity Ann Sattler
- University of Natural Resources and Applied Life Sciences, Department for Agrobiotechnology, Tulln, Austria
- * E-mail:
| | | | - Viviana Klose
- University of Natural Resources and Applied Life Sciences, Department for Agrobiotechnology, Tulln, Austria
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Effects of Propionibacterium strains on ruminal fermentation, nutrient digestibility and methane emissions in beef cattle fed a corn grain finishing diet. Animal 2014; 8:1807-15. [DOI: 10.1017/s1751731114001657] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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15
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Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments. Appl Microbiol Biotechnol 2013; 97:7553-62. [PMID: 23877581 DOI: 10.1007/s00253-013-5102-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/05/2013] [Accepted: 07/05/2013] [Indexed: 10/26/2022]
Abstract
Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.
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Quantitative detection of viable Bifidobacterium bifidum BF-1 cells in human feces by using propidium monoazide and strain-specific primers. Appl Environ Microbiol 2013; 79:2182-8. [PMID: 23354719 DOI: 10.1128/aem.03294-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We developed a PCR-based method to detect and quantify viable Bifidobacterium bifidum BF-1 cells in human feces. This method (PMA-qPCR) uses propidium monoazide (PMA) to distinguish viable from dead cells and quantitative PCR using a BF-1-specific primer set designed from the results of randomly amplified polymorphic DNA analysis. During long-term culture (10 days), the number of viable BF-1 cells detected by counting the number of CFU on modified MRS agar, by measuring the ATP contents converted to CFU, and by using PMA-qPCR decreased from about 10(10) to 10(6) cells/ml; in contrast, the total number of (viable and dead) BF-1 cells detected by counting 4',6-diamidino-2-phenylindolee (DAPI)-stained cells and by using qPCR without PMA and reverse transcription-qPCR remained constant. The number of viable BF-1 cells in fecal samples detected by using PMA-qPCR was highly and significantly correlated with the number of viable BF-1 cells added to the fecal samples, within the range of 10(5.3) to 10(10.3) cells/g feces (wet weight) (r > 0.99, P < 0.001). After 12 healthy subjects ingested 10(10.3) to 10(11.0) CFU of BF-1 in a fermented milk product daily for 28 days, 10(4.5 ± 1.5) (mean ± standard deviation [SD]) BF-1 CFU/g was detected in fecal samples by using strain-specific selective agar; in contrast, 10(6.2 ± 0.4) viable BF-1 cells/g were detected by using PMA-qPCR, and a total of 10(7.6 ± 0.7) BF-1 cells/g were detected by using qPCR without PMA. Thus, the number of viable BF-1 cells detected by PMA-qPCR was about 50 times higher (P < 0.01) than that detected by the culture-dependent method. We conclude that strain-specific PMA-qPCR can be used to quickly and accurately evaluate viable BF-1 in feces.
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Sirohi SK, Singh N, Dagar SS, Puniya AK. Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem. Appl Microbiol Biotechnol 2012; 95:1135-54. [PMID: 22782251 DOI: 10.1007/s00253-012-4262-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/20/2012] [Accepted: 06/22/2012] [Indexed: 12/30/2022]
Abstract
Rumen microbial community comprising of bacteria, archaea, fungi, and protozoa is characterized not only by the high population density but also by the remarkable diversity and the most complex microecological interactions existing in the biological world. This unprecedented biodiversity is quite far from full elucidation as only about 15-20 % of the rumen microbes are identified and characterized till date using conventional culturing and microscopy. However, the last two decades have witnessed a paradigm shift from cumbersome and time-consuming classical methods to nucleic acid-based molecular approaches for deciphering the rumen microbial community. These techniques are rapid, reproducible and allow both the qualitative and quantitative assessment of microbial diversity. This review describes the different molecular methods and their applications in elucidating the rumen microbial community.
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Affiliation(s)
- Sunil Kumar Sirohi
- Nutrition Biotechnology Laboratory, Dairy Cattle Nutrition Division, National Dairy Research Institute, Karnal, 132001, Haryana, India.
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