Identification of a Candidate Starch Utilizing Strain of Prevotella albensis from Bovine Rumen.

Venkata Vinay Kumar Bandarupalli,Benoit St-Pierre

doi:10.3390/microorganisms8122005

Venkata Vinay Kumar Bandarupalli, Benoit St-Pierre

Open Access

https://doi.org/10.3390/microorganisms8122005

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Abstract

The inclusion of starch-rich feedstuffs, a common practice in intensive ruminant livestock production systems, can result in ruminal acidosis, a condition that can severely impact animal performance and health. One of the main causes of acidosis is the rapid accumulation of ruminal short chain fatty acids (SCFAs) resulting from the microbial digestion of starch. A greater understanding of ruminal bacterial amylolytic activities is therefore critical to improving mitigation of acidosis. To this end, our manuscript reports the identification of a candidate starch utilizer (OTU SD_Bt-00010) using batch culturing of bovine rumen fluid supplemented with starch. Based on 16S rRNA gene sequencing and metagenomics analysis, SD_Bt-00010 is predicted to be a currently uncharacterized strain of Prevotella albensis. Annotation of de novo assembled contigs from metagenomic data not only identified sequences encoding for α-amylase enzymes, but also revealed the potential to metabolize xylan as an alternative substrate. Metagenomics also predicted that SCFA end products for SD_Bt-00010 would be acetate and formate, and further suggested that this candidate strain may be a lactate utilizer. Together, these results indicate that SD_Bt-00010 is an amylolytic symbiont with beneficial attributes for its ruminant host.

Highlights

As a result of their ability to produce high-quality protein products such as milk and meat from plant fibers, which cannot be efficiently digested by humans, ruminants have so far played a vital role throughout human history, and they are expected to continue to do so in the foreseeable future [1,2]
The latter makes use of BLAST [30] to compare each operational taxonomic units (OTUs) to its closest match in the “nt” database from the National Center for Biotechnology Information (NCBI); if an OTU has more than five nucleotides missing from the 5 or 3 end of its alignment, it is removed from the analysis
Analysis of rumen fluid inocula before culturing with starch revealed that bacteria affiliated to the phyla Bacteroidetes (E1 = 51.0%; Experiment 2 (E2) = 24.8%) and Firmicutes (E1 = 36.6%; E2 = 68.2%) were overall the most abundant in the donors used in this study (Figure 1)

Summary

Introduction

As a result of their ability to produce high-quality protein products such as milk and meat from plant fibers, which cannot be efficiently digested by humans, ruminants have so far played a vital role throughout human history, and they are expected to continue to do so in the foreseeable future [1,2] In these herbivores, the digestion of feed takes place in the rumen, the largest compartment of a four-chambered stomach, through the combined metabolic activities of resident microbial symbionts which precede digestion by host enzymes [3,4]. Metagenomics predicted that SCFA end products for SD_Bt-00010 would be acetate and formate, and suggested that this candidate strain may be a lactate utilizer Together, these results indicate that SD_Bt-00010 is an amylolytic symbiont with beneficial metabolic attributes for its ruminant host

Sample Collection and In Vitro Rumen Culture Experiments

Microbial Genomic DNA Purification and PCR Amplification of the 16S rRNA Gene

Bioinformatic Analysis for 16S rRNA Gene-Based Composition Analysis

Metagenomics Analysis

Comparative Analysis of Bacterial Communities from Rumen Fluid Donors

Discussion