Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling

Eikmeyer, Felix Gregor; Köfinger, Petra; Poschenel, Andrea; Jünemann, Sebastian; Zakrzewski, Martha; Heinl, Stefan; Mayrhuber, E.; Grabherr, Reingard; Pühler, Alfred; Schwab, Helmut; Schlüter, Andreas

doi:10.1016/j.jbiotec.2013.07.021

Cited by 115 publications

(118 citation statements)

References 41 publications

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“…These observations are in accordance with our results as the core bacterial microbiome after 90 day of fermentation in silage showed reduced diversity and was largely dominated by members of the Lactobacillales. Using 16S pyrosequencing and metagenomic analysis, Eikmeyer et al [23] observed a predominance of bacteria from the phylum Firmicutes in grass silage after 58 days of ensiling. Members of the Lactobacillales, including Lactococcus , Lactobacillus and Weissella accounted for 80% of relative bacterial abundance, a result similar to our observations.…”

Section: Discussionmentioning

confidence: 99%

“…Ribosomal DNA (rDNA) gene sequencing has been successfully used in many studies to describe microbiomes in complex environments including the rhizosphere [17, 18], soil [19, 20], compost [21] and rumen [22]. Eikmeyer et al [23] were the first to study the bacterial microbiome of grass silage during ensiling with and without inoculants. However, these authors focused only on bacterial communities and did not describe the nature of the fungal microbiome.…”

Section: Introductionmentioning

confidence: 99%

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Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Dunière¹,

Xu²,

Jin³

et al. 2017

BMC Microbiol

122

109

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BackgroundDescribing the microbial populations present in small grain silage and understanding their changes during ensiling is of interest for improving the nutrient value of these important forage crops. Barley, oat and triticale forages as well as an intercropped mixture of the 3 crops were harvested and ensiled in mini silos for a period of 90 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics and nutritive value were assessed in terminal silages and bacterial and fungal communities during ensiling and aerobic exposure were described using 16S and 18S rDNA sequencing, respectively.ResultsAll small grain silages exhibited chemical traits that were associated with well ensiled forages, such as low pH value (4.09 ± 0.28) and high levels of lactic acid (59.8 ± 14.59 mg/g DM). The number of microbial core genome operational taxonomic units (OTUs) decreased with time of ensiling. Taxonomic bacterial community profiles were dominated by the Lactobacillales after fermentation, with a notable increase in Bacillales as a result of aerobic exposure. Diversity of the fungal core microbiome was shown to also be reduced during ensiling. Operational taxonomic units assigned to filamentous fungi were found in the core microbiome at ensiling and after aerobic exposure, whereas the Saccharomycetales were the dominate yeast population after 90 days of ensiling and aerobic exposure. Bacterial and fungal orders typically associated with silage spoilage were identified in the core microbiome after aerobic exposure.ConclusionNext Generation Sequencing was successfully used to describe bacterial communities and the first record of fungal communities throughout the process of ensiling and utilization. Adequately describing the microbial ecology of silages could lead to improved ensiling practices and the selection of silage inoculants that act synergistically with the natural forage microbiome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-0947-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Dunière¹,

Xu²,

Jin³

et al. 2017

BMC Microbiol

122

109

View full text Add to dashboard Cite

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“…Ennahar et al found that Firmicutes was the predominate phylum in the pin paddy rice silage, and most of the reads at the phylum level were assigned to the genus Lactobacillus, Laxtococcus and Weissella (Ennahar et al, 2003). The dominant species were identified as Lactococcuslactis, Lactobacillus brevis and Lactobacillus plantarum in the grass silage (Eikmeyer et al, 2013).…”

Section: Chemical Composition Of Ensilaged Samplesmentioning

confidence: 99%

Effect of microalgae supplementation on the silage quality and anaerobic digestion performance of Manyflower silvergrass

Sun

Yuan

et al. 2015

Bioresource Technology

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“…Recent advances in genome sequencing of this species have shed light on the molecular underpinnings that allow L. buchneri to withstand the pickling process. In particular, determining the complete genome sequences of strains NRRL B-30929 and CD034 (3)(4)(5) established several genetic loci for substrate utilization pathways (notably, those for lactate and carbohydrates), including the ability to convert lactic acid into acetic acid (5) and 1,2-propanediol (2). Conversely, the biochemical properties of this robust bacterium have been exploited for silage inoculation to control yeast and mold growth under anaerobic conditions during the fermentation of corn, barley, wheat, and other grains into animal fodder (5)(6)(7).…”

mentioning

confidence: 99%

Lactobacillus buchneri Genotyping on the Basis of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Locus Diversity

Briner

Barrangou

2014

Appl Environ Microbiol

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Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel "spacers" that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5=-AAAA-3=. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri.T he pickle industry relies on the use of naturally occurring bacteria for the fermentation of cucumbers in large industrial tanks (1). To control the diverse microbiota naturally associated with pickles and to preclude spoilage by undesirable microorganisms, salting and brining are implemented in industrial settings. Unfortunately, acid-and halotolerant lactic acid bacteria often contaminate the pickling process, resulting in a secondary fermentation, which spoils the product by generating undesirable attributes (1). Among commonly encountered bacterial contaminants, Lactobacillus buchneri has repeatedly been associated with spoilage of fermenting pickles (1, 2). Recent advances in genome sequencing of this species have shed light on the molecular underpinnings that allow L. buchneri to withstand the pickling process. In particular, determining the complete genome sequences of strains NRRL B-30929 and CD034 (3-5) established several genetic loci for substrate utilization pathways (notably, those for lactate and carbohydrates), including the ability to convert lactic acid into acetic acid (5) and 1,2-propanediol (2). Conversely, the biochemical properties of this robust bacterium have been exploited for silage inoculation to control yeast and mold growth under anaerobic conditions during the fermentation of corn, barley, wheat, and other grains into animal fodder (5-7).Bacteria used in industrial settings for fermentation purposes are often challenged by ubiquitous bacteriophages, whic...

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Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling

Cited by 115 publications

References 41 publications

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Effect of microalgae supplementation on the silage quality and anaerobic digestion performance of Manyflower silvergrass

Lactobacillus buchneri Genotyping on the Basis of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Locus Diversity

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