Biology subjects

Santos-Bay, L.

Publications and source records attributed to Santos-Bay, L..

5 recordsLinked to original sources

bioRxiv2025

The effect of different milk pretreatment methods on microbiome community development during Herrgards cheese production and ripening.

One of the biggest challenges for dairy producers is the substantial variability in final product properties caused by changes in the production environment. In cheese production, this variation is influenced by several factors, particularly the milk base and its pretreatment, which shape the microbiome throughout the process and ultimately affect the cheeses organoleptic characteristics. To examine the impact of three different pre-treatments for pasteurised milk-- microfiltration, protein fortification, and only pasteurisation (control)-- on microbiome dynamics, we generated metagenome sequencing data from 14 cheese production steps across these three production trials at a Danish dairy factory. We constructed three metagenomic co-assemblies, identifying nine high-quality metagenome-assembled genomes (MAGs). Our analysis revealed that a specific strain of Lactococcus lactis dominates the process, while other minor bacterial species persist at very low abundances (<1%), contributing non-negligibly to product properties. Notably, Clostridium tyrobutyricum, a known dairy spoilage bacterium, was present at low levels in pasteurised-only and protein-fortified milk trials but was nearly absent in microfiltered milk. To enhance our analyses, we implemented KHILL, a novel k-mer-based method applied directly to raw sequencing reads, which facilitates metagenomic co-assembly and enables early detection of unwanted microorganisms. Our findings provide industrial dairy producers with a comprehensive view of microbial dynamics during cheese production, offering insights to improve process consistency and product quality.

microbiology↗

bioRxiv2024

Functional insights into the effect of feralisation on the gut microbiota of cats worldwide

Feralisation, the process by which domesticated organisms revert to a wild state, is a widespread phenomenon across various species. Successfully adapting to a new environment with different access to food, shelter, and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 draft genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed distinct taxonomic and functional profiles between the two groups. While taxonomic enrichment was balanced, microbial functional capacities were significantly enriched in feral cats. These functional enhancements, particularly in amino acid and lipid degradation, correspond to feral cats dietary reliance on crude protein and fat. Additionally, functional differences were consistent with behavioural contrasts, such as the more aggressive and elusive behaviour measured in feral cats compared to the docile behaviour of domestic cats. Finally, the observed enrichment in short-chain fatty acid, neurotransmitter, and vitamin B12 production in feral cats aligns with improved cognitive function and potentially contributes to their heightened aggression and elusiveness. Our findings suggest that microbiome shifts may play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, supporting the adaptive success of feral cats in the wild.

evolutionary biology↗

bioRxiv2023

A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics

Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 faecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: i) 20 Gbp of Illumina short-read data, ii) 40 Gbp of short-read data, iii) 20 Gbp of PacBio HiFi long-read data, and iv) 40 Gbp of hybrid (20 Gbp of short-read + 20 Gbp of long-read) data. No strategy was best for all metrics, but instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies, and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific, and depends on how researchers assess the tradeoff between the quantity and quality of recovered genomes. ImportanceOur understanding of microbial communities is limited by the technologies we employ. Here, we test several different DNA sequencing techniques to better understand the pros and cons of each. Long read DNA sequencing allowed for the reconstruction of higher quality and even complete microbial genomes, however, the cost was greater than commonly used short-read DNA sequencing. We suggest researchers consider the trade-offs between each method and decide based on the goals of their research question/s.

microbiology↗

bioRxiv2023

Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon

Animals and their associated microbiota share long evolutionary histories. Both host genotype and associated microbiota influence phenotypes such as growth and disease resilience. We applied a hologenomic approach to explore the relationship between host and microbiota in shaping lifetime growth and parasitic cestode infection in farmed Atlantic salmon. Genomes, transcriptomes, metabolomes and metagenomes were generated from the guts of 460 harvest-aged salmon, 82% of which were naturally infected with an intestinal cestode. One salmonid-specific Mycoplasma dominated the gut microbiota of uninfected salmon. However, the microbiota was perturbed in smaller, parasitised fish, with increased abundance of Vibrionaceae and other Mycoplasma species previously linked to the cestode microbiota. The cestode-associated Mycoplasma carry more virulence-associated genes than the salmonid Mycoplasma. Colonisation by one cestode-associated Mycoplasma was associated with a region of the salmon genome encoding several long noncoding RNA genes previously associated with host control of intestinal microbiota. Integrating the multiple omic datasets revealed coordinated changes in the salmon gut transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitised fish. Our results suggest that cestode infections introduce new microbes and trigger host responses, altering the gut microbiota with increases in potentially pathogenic microbes. Establishment of these microbes is partially shaped by the genetic background of the host. Our study highlights the value of a hologenomic approach for gaining an in-depth understanding of trilateral interactions among host, microbiota and parasite.

systems biology↗

bioRxiv2022

The genomic basis of the plant island syndrome in Darwin's giant daisies

Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounced phenotypic changes. Repeated patterns of evolutionary change in plants on oceanic archipelagos, i.e. the plant island syndrome, include changes in leaf morphology, acquisition of perennial life-style, and change of ploidy. Here, we describe the genome of the critically endangered and Galapagos endemic Scalesia atractyloides Arnot., obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galapagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in Darwins giant daisy radiation. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterizes the quick and pronounced genomic changes in a specular and diverse radiation of an iconic island plant radiation.

evolutionary biology↗