Biology subjects

Bloomfield, S. J.

Publications and source records attributed to Bloomfield, S. J..

3 recordsLinked to original sources

bioRxiv2025

Tissue destruction during food spoilage is associated with the formation of biofilms by Pseudomonas species

Members of the Pseudomonas genus are common spoilers of a range of meat, dairy and vegetable products. While we have a good understanding of the Pseudomonas species typically responsible for spoilage, we know very little about how these bacteria interact with food surfaces during spoilage. Here we assessed the spoilage capabilities of a large panel (n=124) of Pseudomonas species food-derived isolates on meat (chicken) and leafy greens (spinach). Most isolates (71/124) were capable of spoiling both foods, but some were only capable of spoiling only chicken (21/124) or spinach (23/124), or neither (9/124). Our data also demonstrated that the type of fresh food the strain was isolated from influenced spoilage capabilities: strains isolated from meat were likely to spoil both chicken and spinach, while those isolated from leafy greens were more likely to spoil only spinach. We used fluorescence microscopy to visualise how Pseudomonas spoilage species interacted with the meat or leaf tissue and observed significant tissue destruction associated with biofilm formation. For chicken, this was associated with the formation of dense biofilm pillars that penetrated deep into the tissue. For spinach we observed biofilms on the leaf in areas of tissue degradation. Finally, we explored the correlation between potentially relevant phenotypes (in vitro biofilm, motility and secreted enzyme production) and spoilage capabilities. There was no significant correlation between any of these phenotypes and spoilage, except for secreted protease activity and chicken spoilage. Overall, this study increases our understanding of processes involved in food spoilage by Pseudomonas species.

microbiology↗

bioRxiv2025

Environmental context as a key driver of Pseudomonas biocontrol activity against Salmonella.

Salmonella poses a significant threat to food security, with frequent outbreaks reported worldwide. A large percentage of these outbreaks are associated with fresh produce intended for raw consumption. Plant microbiomes harbour diverse microbial communities, including commensal microbes such as Pseudomonas that sometimes exhibit biocontrol activity against plant pathogens. However, little is known about whether Pseudomonas strains can effectively suppress foodborne pathogens and the mechanisms they employ. In this study, we identified and characterised food derived Pseudomonas isolates capable of inhibiting Salmonella growth in vitro and in planta. The identified isolates were active against a range of Salmonella serovars, and additionally E. coli isolates derived from food. We demonstrated that dynamics of the interaction between Pseudomonas and Salmonella are environment and application dependant. To uncover the mechanisms Pseudomonas employs to suppress Salmonella, we used transcriptomics coupled with pathway analysis in the two different settings. We showed that Pseudomonas metabolism undergoes significant environment-specific changes in the presence of Salmonella, implicating different pathways responsible for the control of the pathogen in the two different settings. Our results highlight the plasticity of Pseudomonas metabolism in response to Salmonella in two distinct environments and provide evidence that Pseudomonas biocontrol activity is multifactorial and environment dependent.

microbiology↗

bioRxiv2024

Lapidary: Identifying and reporting amino acid sequences in metagenomes using sequence reads and Diamond

Genome and metagenome comparisons rely on identifying genetic elements that differ or are in common between samples. These genetic elements can be identified by assembling sequenced reads and identifying the genetic element in the assembly, or by aligning nucleotide sequences in the reads to the nucleotide sequences of a reference genetic element. The first relies on the complete assembly of the genetic element of interest, and the second relies on a reference sequence represented in nucleotides. This is particularly challenging with metagenome data, where the genetic elements, including genes, are often fragmented because sequences are shared between different species in the metagenomic data, resulting in contig breaks in or around genetic elements. This presents a difficulty when identifying genetic elements through the first approach. A common approach with metagenomes is to map reads against reference nucleotide sequences and extract the depth and coverage from those reference sequences. However, currently no software exists to identity and report genetic elements using DNA-protein alignments in metagenomes. We have developed the software Lapidary to identify the identity, coverage, depth, and most likely sequence of amino acid sequences from both genome and metagenome read files. We tested the effectiveness of the method against simulated, genomic and metagenomic read datasets. Lapidary is more sensitive than assembly methods for metagenomic data that often have fragmented assemblies but is less sensitive when assemblies are more complete, as is the case with genomic data.

bioinformatics↗