Taxonomic and Functional Shifts in the Sprout Spent Irrigation Water Microbiome in Response to Salmonella Contamination of Alfalfa Seeds

Abstract

Despite recent advances in Salmonella-sprout research, little is known about the relationship between Salmonella and the sprout microbiome during sprouting. Sprout spent irrigation water (SSIW) provides an informative representation of the total microbiome of this primarily aquaponic crop. This study was designed to characterize the function and taxonomy of the most actively transcribed genes in SSIW from Salmonella Cubana contaminated alfalfa seeds throughout the sprouting process. Genomic DNA and total RNA from SSIW was collected at regular intervals and sequenced using Illumina Miseq and NextSeq platforms. Nucleic acid data were annotated using four different pipelines. Both metagenomic and metatranscriptomic analyses revealed a diverse and highly dynamic SSIW microbiome. A ‘core’ SSIW microbiome comprised Klebsiella, Enterobacter, Pantoea, and Cronobacter. The impact, however, of Salmonella contamination on alfalfa seeds influenced SSIW microbial community dynamics not only structurally but also functionally. Changes in genes associated with metabolism, genetic information processing, environmental information processing, and cellular processes were abundant and time dependent. At time points of 24 h, 48 h, and 96 h, a total of 541, 723, and 424 S. Cubana genes, respectively, were transcribed at either higher or lower levels compared with S. Cubana at 0 h in SSIW during sprouting. An array of S. Cubana genes (107) were induced at all three time points including genes involved in biofilm formation and modulation, stress responses, and virulence and tolerance to antimicrobials. Taken together, these findings expand our understanding of the effect of Salmonella seed contamination on the sprout crop microbiome and metabolome. IMPORTANCE Interactions of human enteric pathogens like Salmonella with plants and plant microbiomes remain to be elucidated. The rapid development of next generation sequencing technologies provides powerful tools enabling investigation of such interactions from broader and deeper perspectives. Using metagenomic and metatranscriptomic approaches, this study not only identified the changes in microbiome structure of SSIW associated with sprouting, but also the changes in the gene expression patterns related to the sprouting process in response to Salmonella contamination of alfalfa seeds. This study advances our knowledge on Salmonella-plant (i.e., sprouts) interaction.

Efficacy of Repeated Applications of Bacteriophages on Salmonella enterica-Infected Alfalfa Sprouts during Germination

“…Alfalfa sprout seeds are naturally abundant with microorganisms from a multitude of bacterial families, namely Enterobacteriacae, Acinetobacter, Janthinobacterium, and Pseudomonas [ 46 ]. E. coli 0157 and non-0157 and Salmonella are all representatives of the Enterobacteriacae family, and all have the potential to naturally be present on alfalfa sprout seeds [ 47 , 48 ]. There is a possibility for the phages in this study to infect distinct but related bacteria in the same family, but conclusions cannot be drawn without further genomic analyses.…”

Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting

“…Libraries were run on the NextSeq 2000 (P2 and P3 300 cycle kits, paired, 2 by 150 bp). Reads were screened/trimmed using Trimmomatic ( 8 ), and an average of ~5 million reads per replicate was annotated using a Food and Drug Administration (FDA) in-house bacterial kmer database (Bactikmer) as previously described ( 9 – 11 ) ( https://github.com/mmammel8/kmer_id , available on http://galaxytrakr.org [ 12 ]). To annotate antimicrobial resistance (AMR), fastqs were run on the AMR++ pipeline with the Megares database v2 ( 13 ) using the Center for Food Safety and Applied Nutrition (CFSAN) high performance cluster (HPC) with default parameters.…”

A comparative analysis of peptide-delivered antisense antibiotics employing diverse nucleotide mimics

“…The experiments were performed by modifying previously published protocols (Ghosh et al 2016;Ellis et al 2019;Zheng et al 2021). Salmonella (WT SL1344, JVS-1574) were grown overnight in 4 ml MHB medium at 37 °C (with shaking at 220 rpm).…”