Use of real time PCR to determine population profiles of individual species of lactic acid bacteria in alfalfa silage and stored corn stover

Stevenson, David; Muck, R. E.; Shinners, K. J.; Weimer, Paul J.

doi:10.1007/s00253-005-0170-z

Cited by 85 publications

(78 citation statements)

References 19 publications

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“…To quantify relative abundances of bacterial species known to be part of the Drosophila microbiome, we performed qPCR analyses with speciesspecific oligonucleotide primer pairs for the following bacterial species: Acetobacter tropicalis (8), Commensalibacter intestini (S-S-C-intest-1018-a-S-19 and S-S-C-intest-1130-a-A-19), Lactobacillus brevis (18), Lactobacillus plantarum (8), and Guconobacter sp. (19).…”

Section: Methodsmentioning

confidence: 99%

Noninvasive Analysis of Microbiome Dynamics in the Fruit Fly Drosophila melanogaster

Fink

Staubach

Kuenzel

et al. 2013

Appl Environ Microbiol

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The diversity and structure of the intestinal microbial community has a strong influence on life history. To understand how hosts and microbes interact, model organisms with comparatively simple microbial communities, such as the fruit fly (Drosophila melanogaster), offer key advantages. However, studies of the Drosophila microbiome are limited to a single point in time, because flies are typically sacrificed for DNA extraction. In order to test whether noninvasive approaches, such as sampling of fly feces, could be a means to assess fly-associated communities over time on the same cohort of flies, we compared the microbial communities of fly feces, dissected fly intestines, and whole flies across three different Drosophila strains. Bacterial species identified in either whole flies or isolated intestines were reproducibly found in feces samples. Although the bacterial communities of feces and intestinal samples were not identical, they shared similarities and obviously the same origin. In contrast to material from whole flies and intestines, feces samples were not compromised by Wolbachia spp. infections, which are widespread in laboratory and wild strains. In a proof-of-principle experiment, we showed that simple nutritional interventions, such as a high-fat diet or short-term starvation, had drastic and long-lasting effects on the micobiome. Thus, the analysis of feces can supplement the toolbox for microbiome studies in Drosophila, unleashing the full potential of such studies in time course experiments where multiple samples from single populations are obtained during aging, development, or experimental manipulations.T he microbial community of the metazoan intestine contributes substantially to the host's nutrition and energy balance (1). Dysregulation of the host-microbiota interaction is associated with various disease states, including chronic inflammation, obesity, or even cancer (2-4). As the complex interplay between host and microbiota is only fragmentarily understood, simple models, such as the fruit fly Drosophila melanogaster, are of particular interest. The fly combines a relatively simple microbial community with an unchallenged armamentarium of methods allowing manipulation of the host (5-7). Recent deep-sequencing approaches using 454 sequencing confirmed the general finding that the bacterial community of lab-reared flies is dominated by slightly more than a few operational taxonomic units (OTUs) (8). In Drosophila, the microbiota has been shown to modulate different aspects of intestinal homeostasis, including stem cell activity and epithelial immunity (9-11). Moreover, the intestinal microbiota influences life span and growth rate (12)(13)(14).These aforementioned studies aiming to characterize the fly microbiome relied on isolation of bacterial material from whole flies or manually dissected intestines. Both approaches are invasive, and the flies must be sacrificed. Noninvasive approaches would offer the advantage that flies could be analyzed throughout their life span or before and after...

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Section: Methodsmentioning

confidence: 99%

Noninvasive Analysis of Microbiome Dynamics in the Fruit Fly Drosophila melanogaster

Fink

Staubach

Kuenzel

et al. 2013

Appl Environ Microbiol

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“…Silage isolates of L. buchneri were approved by the FDA in 2001 to use as bacterial inoculants for ensilaging various grains [8-11, 22, 29]. These strains generally produce high levels of acetic acid with other unidentiWed products [1,2,18,27,32], although another silage isolate, L. buchneri strain NK01, metabolizes lactate with accumulation of substantial amounts of 1,2-propanediol [19]. A sour dough isolate, L. buchneri strain B190, produces 1,3-propanediol from glycerol [24,30,31].…”

Section: Introductionmentioning

confidence: 99%

Lactobacillus buchneri strain NRRL B-30929 converts a concentrated mixture of xylose and glucose into ethanol and other products

Liu

Skinner-Nemec

Leathers

2007

J Ind Microbiol Biotechnol

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Lactobacillus buchneri strain NRRL B-30929 was isolated from a fuel ethanol production facility. This heterofermentative, facultative anaerobe can utilize xylose as a sole carbon source and tolerates up to 12% ethanol. Carbohydrate utilization (API, Biomerieux) and Phenotype Microarrays (PM, Biolog) analyses indicated that the strain is able to metabolize a broad spectrum of carbon sources including various monosaccharides (C5 and C6), disaccharides and oligosaccharides, with better rates under anaerobic conditions. In pH-controlled bioreactors, the bacterium consumed xylose and glucose simultaneously at high concentrations (125 g L(-1), pH 6.0). The major fermentation products were lactate (52 g L(-1)), acetate (26 g L(-1)) and ethanol (12 g L(-1)). The strain ferments glucose alone (pH 4.0) into lactate and ethanol with a molar ratio of 1.03:1. This strain will be further explored via genetic engineering for potential applications in biomass conversion.

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“…Although these indicators may partially reflect the silage quality, the assessment process is time-consuming and the results are sometimes inaccurate, especially because of the limited information obtained regarding the silage microbial composition. Recently, real-time polymerase chain reaction and in-depth 16S rRNA gene libraries sequence analysis have been designed to quantify the bacterial microbiota of silages prepared with or without commercial inoculants910. These studies have demonstrated the applicability of using such molecular techniques in quantifying certain silage-specific species under a wide variety of conditions.…”

mentioning

confidence: 99%

Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters

Bao

et al. 2016

Sci Rep

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The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.

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Use of real time PCR to determine population profiles of individual species of lactic acid bacteria in alfalfa silage and stored corn stover

Cited by 85 publications

References 19 publications

Noninvasive Analysis of Microbiome Dynamics in the Fruit Fly Drosophila melanogaster

Noninvasive Analysis of Microbiome Dynamics in the Fruit Fly Drosophila melanogaster

Lactobacillus buchneri strain NRRL B-30929 converts a concentrated mixture of xylose and glucose into ethanol and other products

Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters

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