Biology subjects

Antunes, B.

Publications and source records attributed to Antunes, B..

5 recordsLinked to original sources

bioRxiv2025

Fermentation of Agricultural By-products and Zinc Supplementation: A Synergistic Approach to Mealworm Microbiome Optimization

The increasing world population has put pressure on food industry to swiftly come up with initiatives that can sustain an increase in the demand for food, which have led to environmentally unsustainable practices. Insects, such as Tenebrio molitor (TM) larvae, have been widely proposed as sustainable alternative sources of protein with less environmental footprint. Insects can be reared with diets featuring low-cost agricultural side-streams, promoting circular economical practices, which can also be fermented to promote the development of probiotic microbiota. The inclusion of probiotics in the diets of insects during rearing has recently been explored to mitigate potential exposure to pathogens, potentially serving as alternatives to antibiotics. The focus of this study was the fermentation of spinach to naturally develop complex probiotic populations to enrich the diet of mealworms, promoting host health, thus resulting in a more nutritious food/feed source, featuring a safer microbiome profile. Sequencing revealed that fermented spinach had increased lactic acid bacteria (LAB), while repressing Pseudomonas. LAB species have been acknowledged and used as probiotics, whereas Pseudomonas populations are often associated with opportunistic resistant infections. Moreover, zinc is an essential element for bacterial microbiomes of many organisms, including insects. As the effects of dietary zinc on insect gut microbiome have been scarcely investigated, we have supplemented our formulated diets with this trace element and fed it to TM larvae for 35 days. While various diet compositions did not affect mealworm mortality, larvae fed spinach-based and zinc-rich diets gained less weight than that of control. Furthermore, higher dosage of zinc-supplementation resulted in significantly higher accumulation in TM larvae and a lower bioaccumulation factor. Sequencing of larvae fed diets supplemented with fermented spinach revealed increased presence of probiotic-associated genera, Lactococcus and Weissella. It was also found that supplementing diets with spinach and zinc significantly modulated the microbiome of larvae.

microbiology↗

bioRxiv2025

Boosting Bug Farms: A Meta-Analysis on Probiotic Effects in Insect Rearing

Interest in insects and food as feed is rapidly growing. With this, however, comes a move towards mass rearing and industrial scale production. This upscaling and industrialisation of the rearing process is likely to result in high density rearing, which in itself facilitates disease spread (Tarwater and Martin, 2001). Furthermore, the fact that these insects are likely to be genetically closely related further increase the risk of infectious disease outbreak (Ekroth et al., 2019; Gibson and Nguyen, 2021). In tackling this risk, it is important that we do not resort to the mass use of antibiotics that has been seen in the livestock industry. Instead, alternative rearing practices should be developed. A practice that has received a huge increase in attention in the last years is the idea that supplementation of insect feed with probiotics could improve insect health and prevent pathogen spread. We carried out a meta-analysis to systematically analyse the data on probiotic supplementation of insects reared for food and feed available to date. The most commonly measured response to probiotic supplementation was body weight gain followed by microbiome diversity. For body weight gain, we collected 71 effect sizes from 28 studies and for microbiome diversity ten effect sizes from six studies. We found that overall, probiotics tended to increase insect growth rate but did not significantly impact microbiome diversity. Our analysis also highlighted two key literature gaps. To date, data are only available on one of the four insect species able to be sold as food in the EU, Tenebrio molitor. Furthermore, there are currently only very few studies that have looked at protection against pathogens by probiotic bacteria in insects reared for food and feed. So far, the data look promising, but data on more insect species and looking at inhibitory effects against pathogens are urgently needed.

microbiology↗

bioRxiv2024

The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is severely constrained by random peptide mixtures

The prevalence of antibiotic-resistant pathogens has become a major threat to public health, requiring swift initiatives for discovering new strategies to control bacterial infections. Hence, antibiotic stewardship and rapid diagnostics, but also the development, and prudent use, of novel effective antimicrobial agents are paramount. Ideally, these agents should be less likely to select for resistance in pathogens than currently available conventional antimicrobials. The usage of antimicrobial Peptides (AMPs), key components of the innate immune response, and combination therapies, have been proposed as strategies to diminish the emergence of resistance. Herein, we investigated whether newly developed random antimicrobial peptide mixtures (RPMs) can significantly reduce the risk of resistance evolution in vitro to that of single sequence AMPs, using the ESKAPE pathogen Pseudomonas aeruginosa (P. aeruginosa) as a model Gram-negative bacterium. Infections of this pathogen are difficult to treat due the inherent resistance to many drug classes, enhanced by the capacity to form biofilms. P. aeruginosa was experimentally evolved in the presence of AMPs or RPMs, subsequentially assessing the extent of resistance evolution and cross-resistance/collateral sensitivity between treatments. Furthermore, the fitness costs of resistance on bacterial growth were studied, and whole-genome sequencing used to investigate which mutations could be candidates for causing resistant phenotypes. Lastly, changes in the pharmacodynamics of the evolved bacterial strains were examined. Our findings suggest that using RPMs bears a much lower risk of resistance evolution compared to AMPs and mostly prevents cross-resistance development to other treatments, while maintaining (or even improving) drug sensitivity. This strengthens the case for using random cocktails of AMPs in favour of single AMPs, against which resistance evolved in vitro, further providing an alternative to classic antibiotics worth pursuing.

microbiology↗

bioRxiv2023

Complex genomic landscape of inversion polymorphism in Europe's most destructive forest pest

In many species, polymorphic inversions underlie complex phenotypic polymorphisms and facilitate local adaptation in the face of gene flow. Multiple polymorphic inversions can co-occur in a genome, but the prevalence, evolutionary significance, and limits to complexity of genomic inversion landscapes remain poorly understood. Here, we examine genome-wide variation in one of Europes most destructive forest pests, the spruce bark beetle Ips typographus, scan for polymorphic inversions, and test whether inversions are involved in key adaptations in this species. We analyzed 240 individuals from 18 populations across the species European range and, using a whole-genome resequencing approach, identified 27 polymorphic inversions covering approximately 28% of the genome. The inversions vary in size and in levels of intra-inversion recombination, are highly polymorphic across the species range, and often overlap, forming a complex genomic architecture. We test several mechanisms, including directional selection, overdominance and associative overdominance that can contribute to the maintenance of inversion polymorphisms in the genome. We show that the heterogeneous inversion landscape is likely maintained by the combined action of several evolutionary forces and that inversions are enriched in odorant receptor genes encoding key elements of recognition pathways for host plants, mates, and symbiotic fungi. Our results indicate that the genome of this major forest pest of growing social, political, and economic importance harbors one of the most complex inversion landscapes described to date posing a question about limits of genomic architecture complexity.

evolutionary biology↗

bioRxiv2022

THE MAJOR ROLE OF JUNCTIONAL DIVERSITY IN THE HORSE ANTIBODY REPERTOIRE

The sequencing of the antibody repertoire (Rep-seq) revolutionized the diversity of antigen B cell receptor studies, allowing deep and quantitative analysis to decipher the role of adaptive immunity in health and disease. Particularly, horse (Equus caballus) polyclonal antibodies have been produced and used since the century XIX to treat and prophylaxis of diphtheria, tuberculosis, tetanus, pneumonia, and, more recently, COVID-19. However, our knowledge about the horse B cell receptors repertories is minimal. We present a deep horse antibody heavy chain repertoire (IGH) characterization of non-immunized horses using HTS technology. In this study, we obtained a mean of 248,169 unique IgM clones and 66,141 unique IgG clones from four domestic adult horses. Rarefaction analysis showed sequence coverage was between 52 and 82% in IgM and IgG isotypes. We observed that besides horses antibody can use all of the functional IGHV genes, around 80% of their antibodies use only three IGHV gene segments, and around 55% use only one IGHJ gene segment. This limited VJ diversity seems to be compensated by the junctional diversity of these antibodies. We observed that the junctional diversity in horses antibodies is highly frequent, present in more than 90% of horse antibodies. Besides this, the length of this region seems to be higher in horse antibodies than in other species. N1 and N2 nucleotides addition range from 0 to 111 nucleotides. In addition, around 45% of the antibody clones have more than ten nucleotides in both N1 and N2 junction regions. This diversity mechanism may be one of the most important in providing variability to the equine antibody repertoire. This study provides new insights regarding horse antibody composition, diversity generation, and particularities compared to other species, such as the frequency and length of N nucleotide addition. This study also points out the urgent need to better characterize TdT in horses and in other species to better understand antibody repertoire characteristics.

immunology↗