Genome Sequence of the Ruminal Bacterium Megasphaera elsdenii

Abstract

Megasphaera elsdenii is a Gram-negative ruminal bacterium. It is being investigated as a probiotic supplement for ruminants as it may provide benefits for energy balance and animal productivity. Furthermore, it is of biotechnological interest due to its capability of producing various volatile fatty acids. Here we report the complete genome sequence of M. elsdenii DSM 20460, the type strain for the species.The anaerobic Gram-negative coccus Megasphaera elsdenii is found in cattle, sheep, and other ruminants. Elsden et al. (2,3) were the first to isolate this strain, and they have already described its capability to produce a variety of volatile fatty acids. This organism is interesting for the chemical industry as a possible biocatalyst, but characterization of its metabolism is also important for understanding the function of the rumen. The spectrum of short-chain carboxylic acids that is produced depends largely on the carbon source used by the microorganism. However, the metabolic pathways which underlie these observations have been unclear until now. Furthermore, carboxylic acids can also be used as carbon sources. For example, lactic acid is among the most preferred substrates of M. elsdenii. This renders this bacterium a very beneficial member of the rumen community. With the uptake of lactic acid, M. elsdenii can relieve acidosis, a dreaded condition of livestock (1).The genome of Megasphaera elsdenii was sequenced with a combination of next-generation sequencing methods. A firstdraft assembly (Roche 454 GS, FLX Titanium; 773,553 reads with a total of 164.6 Mb; 68-fold coverage) generated with Newbler 2.5.3 consisted of 56 contigs, which could be joined into 1 scaffold. To improve the quality of the sequence by eliminating the 454 sequencing errors in homopolymer stretches, the genome was subsequently sequenced using the Illumina paired-end method (HiSeq 2000; 13,481,796 reads with a total of 1.35 Gb; 558-fold coverage). The Illumina reads were aligned to the already-assembled scaffold with the Genomics Workbench 4.7.1 program (CLC, Aarhus, Denmark). The final consensus sequence was derived by counting instances of each nucleotide at a position and then letting the majority decide the nucleotide in the consensus sequence.The annotation was performed using Prodigal gene finder (5), tRNAscan-SE 1.21 (7), and RNAmmer 1.2 (6). Additionally, the origin of replication was predicted with OriginX (11), and the genome was scanned against Rfam to find other small RNA species. Functional annotation of the predicted genes was performed using a reciprocal best-hit strategy (8) against a group of phylogenetically related organisms. In addition, the putative proteins were searched against Uniprot, Clusters of Orthologous Groups (COG) (9), Pfam (4), and Superfam (10) databases.The draft genome includes 2,474,718 bases, with a GC content of 53%. The number of putative genes totals 2,220, with an average GC content in the coding regions of 54%. There are seven instances of the ribosomal 5S-23S-16S cluster, and 64 predicted...

Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies

“…These have been studied for a variety of reasons including improving fermentative succinate production Draft genomes assembled from metagenomic data (Hess et al, 2011) are also available for rumen bacteria belonging to the following orders: Bacteroidales (5), Clostridiales (7), Myxococcales (1) and Spirochaetales (2). Leahy, Kelly, Ronimus, Wedlock, Altermann and Attwood (Hong et al, 2004;McKinlay et al, 2010), understanding their role in environmental sulphate reduction, characterization of taxonomically unusual organisms (Pukall et al, 2009) and lactate utilization and potential probiotic usage (Marx et al, 2011). However, most bacteria have been investigated because of their role in the processes of plant polysaccharide degradation and SCFA production, which are central to the growth and productivity of ruminant animals.…”

“…These have been studied for a variety of reasons including improving fermentative succinate production (Marx et al, 2011). However, most bacteria have been investigated because of their role in the processes of plant polysaccharide degradation and SCFA production, which are central to the growth and productivity of ruminant animals.…”

Ruminal microorganism consideration and protein used in the metabolism of the ruminants: A review

“…(5) Lactic: Growing under conditions of low rumen pH and using, among others, lactic acid as an energy substrate. Marx et al (2011), for example: Megasphaera elsdenii is a lactate-utilizing bacterium whose ruminal abundance has been shown to be greatly elevated during milk fat depression. Second Weimer et al (2015) studied the effects of the addition of M. elsdenii and concluded milk yield and composition were not affected by dosing.…”

Aspects of Acidosis in Ruminants with a Focus on Nutrition: A Review

“…This drop implies that many gram-negative bacteria, being sensitive to low due to their pH sensitivity, disappear, including lactate-consuming bacteria, like Megasphaera elsdenii and Selenomonas ruminantium (which convert lactate to pyruvate). The lactic acid bacteria growing under conditions of low rumen pH utilize lactic acid as an energy substrate, in addition to other substrates (Marx et al, 2011). Conversely, there is an increase in the population of some gram-positive bacteria, especially Streptococcus bovis, also known as lactate-producing bacteria.…”