title: Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage.
abstract: Describing 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.
  
  
  
  All 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.
  
  
  
  Next 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.
authors.affiliation: Agriculture and Agri-Food Canada Research Centre, Lethbridge, T1J 4B1, AB, Canada.
authors.forename: Lysiane
authors.initials: L
authors.lastname: Duniere
authors.affiliation: Agriculture and Agri-Food Canada Research Centre, Lethbridge, T1J 4B1, AB, Canada.
authors.forename: Shanwei
authors.initials: S
authors.lastname: Xu
authors.affiliation: Agriculture and Agri-Food Canada Research Centre, Lethbridge, T1J 4B1, AB, Canada.
authors.forename: Jin
authors.initials: J
authors.lastname: Long
authors.affiliation: Agriculture and Agri-Food Canada Research Centre, Lethbridge, T1J 4B1, AB, Canada.
authors.forename: Chijioke
authors.initials: C
authors.lastname: Elekwachi
authors.affiliation: Agriculture and Agri-Food Canada Research Centre, Lethbridge, T1J 4B1, AB, Canada.
authors.forename: Yuxi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Agriculture and Agri-Food Canada (AAFC), Lacombe, T4L 1 W1, AB, Canada.
authors.forename: Kelly
authors.initials: K
authors.lastname: Turkington
authors.affiliation: Agriculture and Agri-Food Canada Research Centre, Lethbridge, T1J 4B1, AB, Canada.
authors.forename: Robert
authors.initials: R
authors.lastname: Forster
authors.affiliation: Agriculture and Agri-Food Canada Research Centre, Lethbridge, T1J 4B1, AB, Canada. tim.mcallister@agr.gc.ca.
authors.forename: Tim A
authors.initials: TA
authors.lastname: McAllister
mesh_terms: D000332:Aerobiosis; D018554:Avena / Q000382:microbiology; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D044822:Biodiversity; D004269:DNA, Bacterial; D004271:DNA, Fungal; D004463:Ecology; D002523:Edible Grain / Q000737:chemistry / Q000382:microbiology*; D005285:Fermentation; D005504:Food Analysis; D005658:Fungi / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D001467:Hordeum / Q000382:microbiology; D019344:Lactic Acid / Q000032:analysis; D064307:Microbiota; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012820:Silage / Q000382:microbiology*; D013696:Temperature; D000066889:Triticale / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial; D004271:DNA, Fungal; D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S; D019344:Lactic Acid
keywords: Aerobic exposure; Bacteria; Barley; Fungi; Microbiome; Oats; Silage; Triticale