Micael Siegert Schimmunech^a, Carolina Deuttner Neumann Barroso^a, Anderson Ferreira Da Cunha^b, Marcelo Mendes Brandão^c, Daniel Cruz^d , Karina Ishida^d, Marcelo Beltrão Molento^a,*
^a Laboratory of Veterinary Clinical Parasitology, Department of Veterinary Medicine, Federal University of Paraná, Curitiba, PR, Brazil. This email address is being protected from spambots. You need JavaScript enabled to view it. 
^b Laboratory of Biochemistry and Applied Genetics, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.
^c Laboratory of Integrative and Systemic Biology, Center of Molecular Biology and Genetic Engineering, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
^d World Animal Protection. São Paulo, SP, Brazil.

Pig farming has a significant environmental impact and generates substantial waste. Conventional wastewater treatment on farms often fails to eliminate pathogens, posing transmission risks. This study examined the microbiome of water samples (n=10) from pig farm environments (n=6) and urban areas (n=4) in Brazil. Pig farm samples were from Itambaracá, Paraná, and Chapecó, Santa Catarina, while urban samples were from Curitiba, Paraná, Joinville, and Santa Catarina. Samples included two from before (UP) and after (DOWN) pig farm presence, and two from a city river (CITY) near pig farms. Urban samples were taken from river sources (n=2) and near metropolitan perimeters (n=2). Proteobacteria dominated 90% of samples, with only one sample (P6) showing Firmicutes as predominant. Two pre-DNA extraction techniques were compared: a commercial kit and membrane vacuum filtration. The commercial kit detected E. coli in all samples and P. aeruginosa in 60%. The vacuum filtration technique found Burkholderiales (64%), Burkholderiaceae (81%), and Acidovorax (40%) to be predominant. The commercial kit showed higher Proteobacteria prevalence (>82%) and 100% Gammaproteobacteria. E. coli O157:H7 and Shigella flexneri 2a str. 301 were detected in all commercial kit samples and one vacuum filtration sample. Urban river source samples exhibited high bacterial diversity (615 genera, 736 species in P1; 640 genera, 802 species in P5) with a predominance of Alphaproteobacteria (52%). Samples from the rivers' final courses had reduced diversity (270 genera, 386 species in P2; 25 genera, 24 species in P6) and Gammaproteobacteria predominance. The comparison between the points before (UP) and after (DOWN) did not result in a noticeable correlation of influence from pig farming on the alteration of microbial composition in the samples. Our results highlight the presence of pathogenic bacteria in the aquatic environment surrounding pig farms and emphasize the potential threat to human, animal, and environmental health.

 

Karina L. Silva-Brandão¹, Julia Cabral Teresa², Clécio Fernando Klitzke, Marcelo M. Brandão³, José Roberto Trigo²

1 Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature Hamburg. Martin-Luther-King-Platz 3, 20421 Hamburg, Germany. Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
2 Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas. Rua Monteiro Lobato 255, Campinas, SP, Brazil.
3 Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas. Av. Cândido Rondon, 400, Campinas, SP, Brazil.

The neotropical swallowtail butterfly Battus polydamas is a specialist on Aristolochia (Aristochiaceae). These plants are rich in natural products such as terpenoids, lignans, β-phenylethylamines (βPEA), aporphine and isoquinoline alkaloids, as well as aristolochic acids (AAs). Larvae of B. polydamas sequester some of these compounds, such as AAs, and transfer them to adults through the pupae. AAs are considered defensive compounds against natural enemies, however, the amount of AA in the larvae's diet has an effect on their performance, which may mean a cost to eating on AA-containing leaves. In the present study we evaluated the performance of B. polydamas larvae fed from 1^st instar through pupation on two host plants with different chemistry composition, A. ringens (which has several diterpenes) and A. gigantea (which has acyclic monoterpenoids and sesquiterpenoids, but no diterpenoids or AAs). Differential gene expression as response to different larval host plants was evaluated in three biological replications of gut and fat body tissues of six 5^th instar larvae. We found significant differences in the survival of larvae feeding on the two host plants; the survival in A. gigantea being significantly higher than survival in A. ringens (GLM binomial, likelihood ratio test, df = 1, χ² = 76.082, P < 0.001). In A. gigantea, 55% of the larvae persisted until pupation, while none of the larva feeding on A. ringens survived. 807 unique contigs identified by their molecular function were upregulated in the gut of larvae fed on A. ringens, while 298 were downregulated. Down-regulated contigs include genes encoding for ribosomal proteins, superoxide dismutase, P450s, UGTs, glutathione S-transferase and many proteases. Upregulated contigs comprise genes encoding for ribosomal proteins, protein farnesyltransferase, Phosphomevalonate kinase, Dolichyl-phosphate-mannose-protein mannosyltransferase 4 and O-glucosyltransferase (possibly involved in AAs metabolization). As expected, larvae of B. polydamas were strongly influenced by host plants exhibiting different concentrations of AAs, with higher concentrations leading to worse larval performance on key fitness components, such as life cycle performance attributes and larval survival. We suggest that there is a threshold of AA concentration in the host plant that larvae can tolerate, and above such a threshold the impact of plant secondary chemicals is no longer beneficial for the larvae, but negative, disrupting their detoxification mechanism.

Data availability

It is necessary to properly cite the data repository (https://doi.org/10.25824/redu/A3GVHV) if you choose to utilise any of the data, script, or information provided in these files.

Luiz Gustavo de Matos^a, Anderson Clayton da Silva Abreu^a, Vanessa Pereira Perez Alonso^e, Juliano Leonel Gonçalves^a, Maristela da Silva do Nascimento^b, Sérgio Bertelli Pflanzer Jr^b, Jonatã Henrique Rezende-de-Souza^b, Chiara Gini^c, Natália Faraj Murad^d, Marcelo Mendes Brandão^d, Nathália Cristina Cirone Silva^a

^aDepartment of Food Science and Nutrition, School of Food Engineering (FEA), Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, Sao Paulo, Brazil
^bDepartment of Food Engineering and Technology, School of Food Engineering (FEA), Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, Sao Paulo, Brazil
^cDepartment of Veterinary Medicine, Università degli Studi di Milano, Lodi, Lombardia, Italy
^dLaboratory of Systemic and Integrative Biology, Center of Molecular Biology and Genetic Engineering, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
^eIndependent researcher, Prague, Czechia

https://doi.org/10.1016/j.microb.2024.100035

The science behind dry-aged meat has increased during the last few years. Differently from wet-aging, where meat is vacuum packed, the dry-aging process happens without packaging or protection, which may change the bacterial diversity of the meat, and this change can alter the sensory characteristics of the meat. Different methods are used to identify the microbial of meat. The most used ones are traditional techniques and the Next Generation Sequencing (NGS), widely used to identify bacteria present in diverse types of food. The aim of this study was to evaluate the bacterial diversity of dry-aged and wet-aged beef by traditional microbiological tests and NGS to compare the bacterial diversity given by those different methodologies, as well as compare their specificity. Beef strip loins (n = 6) were collected directly from the slaughterhouse and transported to the laboratory. Samples were dry or wet-aged for 20 and 34 days. Before and after aging, samples were analyzed by Traditional microbiological analysis and NGS. It was observed, with traditional microbiology tests, a greater increase of total bacterial count in the wet-aged samples from 0 to 20 and 34 days, with psychotropic bacteria having the greatest increase. In the dry-aged samples there was a decrease in the total bacterial count, with only molds and yeast significant growth during aging. No E. coli growth was observed for any treatment. From metagenomics analysis, eleven main bacterial genera were detected in the meat microbiota, with a relative abundance higher than 2%, and the seven most abundant ones were Carnobacterium (47.9%), Pseudomonas (22.2%), Lactobacillus (5.4%), Romboutsia (2.8%), Leuconostoc (2.5%), Candidatus Nitrosotalea (2.4%) and Akkermansia (2.3%). Alpha diversity showed a higher richness on the non-aged samples, whereas wet-aged samples showed the smallest richness, the same for the samples aged for 34 days. In addition, beta diversity showed that the microorganisms are highly related when considering time, but different clustering when comparing aging types. Further, dry-aged beef showed a higher presence of Pseudomonas sp., which is a group of microorganisms with a large range of ideal bacterial growth conditions, whereas the wet-aged samples, due to their controlled anaerobic environment, a higher presence of Carnobacterium was observed. It was possible to observe that traditional microbiology is still an important tool in food safety, once it could clearly identify the main important groups of bacteria, once the microorganisms present in food are already very well described, allowing researchers and producers, depending on the methodology used, to check for them, while NGS show more groups, however, it is still an expensive tool, when considering the number of samples. Even showing different data between them, they were both efficient to differentiate the microbiota of the beef samples in their own specificity.

¹Rezende, G.S; ²Funnicelli, M.I.G;³Rocha, F.I ¹Malavazi, I; ^4,5Crauwels, S.; ⁶Brandao, M.M.; ¹Cunha, A.F.

1 Genetic and Evolution Department, Laboratory of Biochemistry and Applied Genetics (LBGA-UFSCar), SP, Brazil;
2 Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
3 Mokichi Okada Research Center/ Korin Agriculture & Environment
4 Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
5 Leuven Institute for Beer Research (LIBR), KU Leuven, Leuven, Belgium
6 Universidade Estadual de Campinas. Centro de Biologia Molecular e Engenharia Genética - Laboratory of integrative and systemic biology (LaBIS- UNICAMP), SP, Brazil

Grapes are globally popular with wine production being one of the most well-known uses of grapes globally. Brazil has a growing wine industry, and the Serra Gaúcha region is a significant contributor to the country's wine production, while other states are also increasing the production. Environmental factors heavily influence grape quality, shaping the crucial "terroir" for wines. Here, the soil quality was assessed through nutrient analysis and microbial diversity, which could significantly impact grape health and final wine attributes. Soil samples from São Paulo's vineyards, focusing on Syrah, Malbec, and Cabernet Sauvignon, underwent physicochemical and microbial analysis via 16S rRNA metabarcoding and highlighted significant differences in soil composition between vineyards. Statistical analyses like PCA and CAP showcased region-based separation and intricate associations between microbiota, region, and grape variety. Correlation analyses pinpointed microbial genera linked to specific soil nutrients. Random Forest analysis identified abundant bacterial genera per grape variety and the Network analyses revealed varied co-occurrence patterns, notably Cabernet Sauvignon exhibiting complex microbial interactions. This study unveils complex relationships between soil microbiota, nutrients, and diverse grape varieties in distinct vineyard regions. Understanding these specific microorganisms associated with grapes holds promise for enhancing vineyard management, grape quality, and wine production, potentially optimizing soil health and bolstering grapevine resilience against pests and diseases, contributing to the unique character of wines known as terroir.

Keywords: Grape; Microbiota; Nutrients, Vineyards; Soil diversity.

Supplementary material:

It is necessary to properly cite the data repository (https://doi.org/10.25824/redu/XCR8XR) if you choose to utilise any of the data, script, or information provided in these files:

Rezende, Graziela Silva; Funnicelli, Michelli Inácio Gonçalves; Rocha, Fernando Igne; Malavazi, Iran; Crauwels, Sam; Brandão, Marcelo Mendes; Cunha, Anderson Ferreira da, 2023, "Supporting material referenced on the manuscript metabarcoding analysis reveals an interaction among distinct groups of bacteria associated with three different varietals of grapes used for wine production in Brazil", https://doi.org/10.25824/redu/XCR8XR

 

Pedro G. Ribeiro^1,2,3, Darli Massardo⁴, Renato Rogner Ramos⁵, Marília B. Lion⁶, Márcio Zikán Cardoso^6,7, Marcus R. Kronforst⁴, André V. L. Freitas⁵, Marcelo Mendes Brandão¹, Karina L. Silva-Brandão^1,8 

¹Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas 13083-875, SP, Brazil;
²Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice 37005, South Bohemia, Czech Republic;
³Faculty of Science, University of South Bohemia, České Budějovice 37005, South Bohemia, Czech Republic;
⁴Department of Ecology & Evolution, The University of Chicago, Chicago 60637, IL, USA;
⁵Departamento de Biologia Animal and Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, SP, Brazil;
⁶Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, RN, Brazil;
⁷Departamento de Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil;
⁸Leibniz Institute for the Analysis of Biodiversity Change, Museum of Natur – Zoology, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany.

 

Amazonian white sand ecosystems (WSEs) are isolated patches of scleromorphic vegetation above white sandy soils that occur exclusively in the Amazon Forest. Due to unique soil characteristics, harsh irradiation, and temperature conditions, these ecosystems present low diversity and high floral and faunal endemism. Nevertheless, they are underrepresented in geological and biological studies, especially regarding the genetic structure and diversity of the species inhabiting them. Here, we investigated the genetic differentiation among populations of Heliconius hermathena Hewitson, 1854 (Lepidoptera, Nymphalidae), a specialized butterfly on the Amazonian white sand ecosystems, as well as their associated Wolbachia endosymbionts. Using the mitochondrial genome, we inferred high levels of genetic differentiation among individuals from six different subspecies of H. hermathena occurring in eight different localities. We also found high levels of structure among H. hermathena populations and postulated that isolation of WSEs and genetic drift must have played an important role in generating and maintaining the species’ current patterns of genetic differentiation. The infection by Wolbachia reached 97% of the specimens, and although isolated both genetically and geographically, the populations investigated share similar Wolbachia contigs. We discuss the importance of habitat isolation for population structure in Amazonia and, therefore, its contribution to the outstanding biodiversity in the region and to the comprehension of the diversification of its endemic species. We also discuss the role of this emblematic species as a model to understand butterfly diversity in isolated environments.

Key words: Amazonia, campinas, mitochondrial genome, Nymphalidae, Wolbachia.

Suplementary Material