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Frank M. Mitloehner - One of the best experts on this subject based on the ideXlab platform.
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Bacterial Population dynamics during the ensiling of medicago sativa alfalfa and subsequent exposure to air
Journal of Applied Microbiology, 2013Co-Authors: Jeffery A. Mcgarvey, R B Franco, Jeffrey D Palumbo, Robert Hnasko, Larry H Stanker, Frank M. MitloehnerAbstract:AIMS To describe, at high resolution, the Bacterial Population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. METHODS AND RESULTS Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their Bacterial Population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P < 0·05) in the Bacterial Populations at each time point. The alfalfa-derived library contained mostly sequences associated with the Gammaproteobacteria (including the genera: Enterobacter, Erwinia and Pantoea); the ensiled material contained mostly sequences associated with the lactic acid bacteria (LAB) (including the genera: Lactobacillus, Pediococcus and Lactococcus). Exposure to air resulted in even greater percentages of LAB, especially among the genus Lactobacillus, and a significant drop in Bacterial diversity. CONCLUSIONS In-depth 16S rRNA gene sequence analysis revealed significant Bacterial Population structure changes during ensiling and again during exposure to air. SIGNIFICANCE AND IMPACT OF THE STUDY This in-depth description of the Bacterial Population dynamics that occurred during ensiling and simulated feed out expands our knowledge of these processes.
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Bacterial Population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air.
Journal of applied microbiology, 2013Co-Authors: Jeffery A. Mcgarvey, R B Franco, Jeffrey D Palumbo, Robert Hnasko, Larry H Stanker, Frank M. MitloehnerAbstract:AIMS To describe, at high resolution, the Bacterial Population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. METHODS AND RESULTS Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their Bacterial Population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P
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Effect of dietary monensin on the Bacterial Population structure of dairy cattle colonic contents
Applied Microbiology and Biotechnology, 2010Co-Authors: Jeffery A. Mcgarvey, Scott W. Hamilton, Edward J. Depeters, Frank M. MitloehnerAbstract:To determine the effect of monensin, a carboxylic polyether ionophore antibiotic, on the Bacterial Population structure of dairy cattle colonic contents, we fed six lactating Holstein cows a diet containing monensin (600 mg day^−1) or an identical diet without monensin. Fresh waste samples were taken directly from the animals once a month for 3 months and assayed for their Bacterial Population structure via 16S rRNA gene sequence analysis. In total 6,912 16S rRNA genes were examined, comprising 345 and 315 operational taxonomic units (OTUs) from the monensin fed and control animals, respectively. Coverage estimates of the OTUs identified were 87.6% for the monensin fed and 88.3% for the control colonic content derived library. Despite this high level of coverage, no significant difference was found between the libraries down to the genus level. Thus we concluded that although monensin is believed to increase milk production in dairy cattle by altering the Bacterial Population structure within the bovine gastrointestinal tract, we were unable to identify any significant difference in the Bacterial Population structure of the colonic contents of monensin fed vs. the control dairy cattle, down to the genus level.
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Bacterial Population Dynamics in Dairy Waste during Aerobic and Anaerobic Treatment and Subsequent Storage
Applied and Environmental Microbiology, 2006Co-Authors: Jeffery A. Mcgarvey, Yanguo Ma, Ruihong Zhang, William G Miller, Frank M. MitloehnerAbstract:The objective of this study was to model a typical dairy waste stream, monitor the chemical and Bacterial Population dynamics that occur during aerobic or anaerobic treatment and subsequent storage in a simulated lagoon, and compare them to those of waste held without treatment in a simulated lagoon. Both aerobic and anaerobic treatment methods followed by storage effectively reduced the levels of total solids (59 to 68%), biological oxygen demand (85 to 90%), and sulfate (56 to 65%), as well as aerobic (83 to 95%), anaerobic (80 to 90%), and coliform (>99%) bacteria. However, only aerobic treatment reduced the levels of ammonia, and anaerobic treatment was more effective at reducing total sulfur and sulfate. The Bacterial Population structure of waste before and after treatment was monitored using 16S rRNA gene sequence libraries. Both treatments had unique effects on the Bacterial Population structure of waste. Aerobic treatment resulted in the greatest change in the type of bacteria present, with the levels of eight out of nine phyla being significantly altered. The most notable differences were the >16-fold increase in the phylum Proteobacteria and the approximately 8-fold decrease in the phylum Firmicutes. Anaerobic treatment resulted in fewer alterations, but significant decreases in the phyla Actinobacteria and Bacteroidetes, and increases in the phyla Planctomycetes, Spirochetes, and TM7 were observed.
Jeffery A. Mcgarvey - One of the best experts on this subject based on the ideXlab platform.
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Bacterial Population dynamics after foliar fertilization of almond leaves
Journal of applied microbiology, 2019Co-Authors: Jeffery A. Mcgarvey, Robert Hnasko, Thao D. Tran, R. Han, Patrick H. BrownAbstract:Aims To describe the effects of foliar fertilizer application on the Bacterial Populations of almond tree leaves. Methods and results We applied a commercially available foliar fertilizer or a water control onto the leaves of almond trees and collected leaves after 1, 7, 14 and 56 days and examined their Bacterial Populations by 16S rRNA gene sequence analysis. After 1 day, we observed significant differences in 3 of the 4 predominant Bacterial phyla, and 5 of the 13 predominant Bacterial families. After 7 days, we observed significant differences in all of the predominant phyla, and 8 of the 13 predominant families. After 14 days, the number of significant differences decreased, and after 56 days only 2 of the 13 predominant families differed significantly. Conclusions Foliar fertilization significantly altered the Bacterial Population structure of almond leaves as compared to the water control. While most of the observed perturbation was transient, significant differences remained after 56 days. Significance and impact of the study This is the first report describing the effects of foliar fertilization on the Bacterial Populations of almond leaves and provides new insights as to how this process alters the leaf Bacterial Population structure.
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Bacterial Population dynamics during the ensiling of medicago sativa alfalfa and subsequent exposure to air
Journal of Applied Microbiology, 2013Co-Authors: Jeffery A. Mcgarvey, R B Franco, Jeffrey D Palumbo, Robert Hnasko, Larry H Stanker, Frank M. MitloehnerAbstract:AIMS To describe, at high resolution, the Bacterial Population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. METHODS AND RESULTS Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their Bacterial Population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P < 0·05) in the Bacterial Populations at each time point. The alfalfa-derived library contained mostly sequences associated with the Gammaproteobacteria (including the genera: Enterobacter, Erwinia and Pantoea); the ensiled material contained mostly sequences associated with the lactic acid bacteria (LAB) (including the genera: Lactobacillus, Pediococcus and Lactococcus). Exposure to air resulted in even greater percentages of LAB, especially among the genus Lactobacillus, and a significant drop in Bacterial diversity. CONCLUSIONS In-depth 16S rRNA gene sequence analysis revealed significant Bacterial Population structure changes during ensiling and again during exposure to air. SIGNIFICANCE AND IMPACT OF THE STUDY This in-depth description of the Bacterial Population dynamics that occurred during ensiling and simulated feed out expands our knowledge of these processes.
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Bacterial Population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air.
Journal of applied microbiology, 2013Co-Authors: Jeffery A. Mcgarvey, R B Franco, Jeffrey D Palumbo, Robert Hnasko, Larry H Stanker, Frank M. MitloehnerAbstract:AIMS To describe, at high resolution, the Bacterial Population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. METHODS AND RESULTS Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their Bacterial Population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P
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Effect of dietary monensin on the Bacterial Population structure of dairy cattle colonic contents
Applied Microbiology and Biotechnology, 2010Co-Authors: Jeffery A. Mcgarvey, Scott W. Hamilton, Edward J. Depeters, Frank M. MitloehnerAbstract:To determine the effect of monensin, a carboxylic polyether ionophore antibiotic, on the Bacterial Population structure of dairy cattle colonic contents, we fed six lactating Holstein cows a diet containing monensin (600 mg day^−1) or an identical diet without monensin. Fresh waste samples were taken directly from the animals once a month for 3 months and assayed for their Bacterial Population structure via 16S rRNA gene sequence analysis. In total 6,912 16S rRNA genes were examined, comprising 345 and 315 operational taxonomic units (OTUs) from the monensin fed and control animals, respectively. Coverage estimates of the OTUs identified were 87.6% for the monensin fed and 88.3% for the control colonic content derived library. Despite this high level of coverage, no significant difference was found between the libraries down to the genus level. Thus we concluded that although monensin is believed to increase milk production in dairy cattle by altering the Bacterial Population structure within the bovine gastrointestinal tract, we were unable to identify any significant difference in the Bacterial Population structure of the colonic contents of monensin fed vs. the control dairy cattle, down to the genus level.
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Bacterial Population Dynamics in Dairy Waste during Aerobic and Anaerobic Treatment and Subsequent Storage
Applied and Environmental Microbiology, 2006Co-Authors: Jeffery A. Mcgarvey, Yanguo Ma, Ruihong Zhang, William G Miller, Frank M. MitloehnerAbstract:The objective of this study was to model a typical dairy waste stream, monitor the chemical and Bacterial Population dynamics that occur during aerobic or anaerobic treatment and subsequent storage in a simulated lagoon, and compare them to those of waste held without treatment in a simulated lagoon. Both aerobic and anaerobic treatment methods followed by storage effectively reduced the levels of total solids (59 to 68%), biological oxygen demand (85 to 90%), and sulfate (56 to 65%), as well as aerobic (83 to 95%), anaerobic (80 to 90%), and coliform (>99%) bacteria. However, only aerobic treatment reduced the levels of ammonia, and anaerobic treatment was more effective at reducing total sulfur and sulfate. The Bacterial Population structure of waste before and after treatment was monitored using 16S rRNA gene sequence libraries. Both treatments had unique effects on the Bacterial Population structure of waste. Aerobic treatment resulted in the greatest change in the type of bacteria present, with the levels of eight out of nine phyla being significantly altered. The most notable differences were the >16-fold increase in the phylum Proteobacteria and the approximately 8-fold decrease in the phylum Firmicutes. Anaerobic treatment resulted in fewer alterations, but significant decreases in the phyla Actinobacteria and Bacteroidetes, and increases in the phyla Planctomycetes, Spirochetes, and TM7 were observed.
Diana Priscila Penso Pires - One of the best experts on this subject based on the ideXlab platform.
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engineering modular viral scaffolds for targeted Bacterial Population editing
Cell systems, 2015Co-Authors: Hiroki Ando, Sebastien Lemire, Diana Priscila Penso PiresAbstract:Bacteria are central to human health and disease, but existing tools to edit microbial consortia are limited. For example, broad-spectrum antibiotics are unable to accurately manipulate Bacterial communities. Bacteriophages can provide highly specific targeting of bacteria, but assembling well-defined phage cocktails solely with natural phages can be a time-, labor- and cost-intensive process. Here, we present a synthetic-biology strategy to modulate phage host ranges by engineering phage genomes in Saccharomyces cerevisiae. We used this technology to redirect Escherichia coli phage scaffolds to target pathogenic Yersinia and Klebsiella bacteria, and conversely, Klebsiella phage scaffolds to target E. coli by modular swapping of phage tail components. The synthetic phages achieved efficient killing of their new target bacteria and were used to selectively remove bacteria from multi-species Bacterial communities with cocktails based on common viral scaffolds. We envision that this approach will accelerate phage-biology studies and enable new technologies for Bacterial Population editing.
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engineering modular viral scaffolds for targeted Bacterial Population editing
bioRxiv, 2015Co-Authors: Hiroki Ando, Sebastien Lemire, Diana Priscila Penso PiresAbstract:Bacteria are central to human health and disease, but the tools available for modulating and editing Bacterial communities are limited. New technologies for tuning microbial Populations would facilitate the targeted manipulation of the human microbiome and treatment of Bacterial infections. For example, antibiotics are often broad spectrum in nature and cannot be used to accurately manipulate Bacterial communities. Bacteriophages can provide highly specific targeting of bacteria, but relying solely on natural phage isolation strategies to assemble well-defined and uniform phage cocktails that are amenable to engineering can be a time-consuming and labor-intensive process. Here, we present a synthetic-biology strategy to modulate phage host ranges by manipulating phage genomes in Saccharomyces cerevisiae. We used this technology to swap multiple modular phage tail components and demonstrated that Escherichia coli phage scaffolds can be redirected to target pathogenic Yersinia and Klebsiella bacteria, and conversely, Klebsiella phage scaffolds can be redirected to target E. coli. The synthetic phages achieved multiple orders-of-magnitude killing of their new target bacteria and were used to selectively remove specific bacteria from multi-species Bacterial communities. We envision that this approach will accelerate the study of phage biology, facilitate the tuning of phage host ranges, and enable new tools for microbiome engineering and the treatment of infectious diseases.
Robert Hnasko - One of the best experts on this subject based on the ideXlab platform.
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Bacterial Population dynamics after foliar fertilization of almond leaves
Journal of applied microbiology, 2019Co-Authors: Jeffery A. Mcgarvey, Robert Hnasko, Thao D. Tran, R. Han, Patrick H. BrownAbstract:Aims To describe the effects of foliar fertilizer application on the Bacterial Populations of almond tree leaves. Methods and results We applied a commercially available foliar fertilizer or a water control onto the leaves of almond trees and collected leaves after 1, 7, 14 and 56 days and examined their Bacterial Populations by 16S rRNA gene sequence analysis. After 1 day, we observed significant differences in 3 of the 4 predominant Bacterial phyla, and 5 of the 13 predominant Bacterial families. After 7 days, we observed significant differences in all of the predominant phyla, and 8 of the 13 predominant families. After 14 days, the number of significant differences decreased, and after 56 days only 2 of the 13 predominant families differed significantly. Conclusions Foliar fertilization significantly altered the Bacterial Population structure of almond leaves as compared to the water control. While most of the observed perturbation was transient, significant differences remained after 56 days. Significance and impact of the study This is the first report describing the effects of foliar fertilization on the Bacterial Populations of almond leaves and provides new insights as to how this process alters the leaf Bacterial Population structure.
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Bacterial Population dynamics during the ensiling of medicago sativa alfalfa and subsequent exposure to air
Journal of Applied Microbiology, 2013Co-Authors: Jeffery A. Mcgarvey, R B Franco, Jeffrey D Palumbo, Robert Hnasko, Larry H Stanker, Frank M. MitloehnerAbstract:AIMS To describe, at high resolution, the Bacterial Population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. METHODS AND RESULTS Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their Bacterial Population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P < 0·05) in the Bacterial Populations at each time point. The alfalfa-derived library contained mostly sequences associated with the Gammaproteobacteria (including the genera: Enterobacter, Erwinia and Pantoea); the ensiled material contained mostly sequences associated with the lactic acid bacteria (LAB) (including the genera: Lactobacillus, Pediococcus and Lactococcus). Exposure to air resulted in even greater percentages of LAB, especially among the genus Lactobacillus, and a significant drop in Bacterial diversity. CONCLUSIONS In-depth 16S rRNA gene sequence analysis revealed significant Bacterial Population structure changes during ensiling and again during exposure to air. SIGNIFICANCE AND IMPACT OF THE STUDY This in-depth description of the Bacterial Population dynamics that occurred during ensiling and simulated feed out expands our knowledge of these processes.
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Bacterial Population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air.
Journal of applied microbiology, 2013Co-Authors: Jeffery A. Mcgarvey, R B Franco, Jeffrey D Palumbo, Robert Hnasko, Larry H Stanker, Frank M. MitloehnerAbstract:AIMS To describe, at high resolution, the Bacterial Population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. METHODS AND RESULTS Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their Bacterial Population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P
Vincent Daubin - One of the best experts on this subject based on the ideXlab platform.
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Reductive genome evolution at both ends of Bacterial Population size spectrum
Nature Reviews Microbiology, 2014Co-Authors: Bérénice Batut, Carole Knibbe, Gabriel Marais, Vincent DaubinAbstract:Bacterial genomes show substantial variations in size. The smallest Bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns consistent with degenerative processes predicted to occur in species with small effective Population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large Populations. Here, we discuss the various hypotheses that have been put forward to account for this reductive genome evolution at both ends of the spectrum of Bacterial Population size.
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reductive genome evolution at both ends of the Bacterial Population size spectrum
Nature Reviews Microbiology, 2014Co-Authors: Bérénice Batut, Carole Knibbe, Gabriel A B Marais, Vincent DaubinAbstract:Bacterial genomes show substantial variations in size. The smallest Bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns consistent with degenerative processes predicted to occur in species with small effective Population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large Populations. Here, we discuss the various hypotheses that have been put forward to account for this reductive genome evolution at both ends of the spectrum of Bacterial Population size.