Rodrigo Jardim

Background/Objectives: Antimicrobial resistance (AMR) is a global health threat, with raw milk serving as a potential reservoir for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). This study characterized the resistome and mobilome of raw milk from cows (Bos taurus) and water buffalo (Bubalus bubalis) in the Brazilian Amazon, a region where unpasteurized dairy consumption is culturally ingrained. Methods: Using shotgun metagenomic sequencing, we analyzed 32 pooled milk samples from extensive and semi-intensive farms in the Manaus Metropolitan Region. Results: Sequencing yielded over 3.1 million contigs. While cow milk showed a higher prevalence of positive samples (80%), buffalo milk exhibited a significantly higher abundance and diversity of ARG-associated contigs (301 contigs vs. 85 in cows). Clinically relevant genes were identified, including AbaQ, ArnT, and KpnF, alongside complex multi-AMR cassettes co-occurring with plasmids and widespread viral sequences (dominated by Caudoviricetes). Integrons were ubiquitous in cattle and highly prevalent in buffalo samples. Conclusions: These findings indicate that raw milk in the Amazon harbors a rich reservoir of resistance determinants and MGEs, likely driven by farm-level antibiotic usage. This underscores a critical food safety risk and highlights the need for One Health-based surveillance in the region.

Glanders is a highly contagious and often fatal zoonotic disease of equids caused by Burkholderia mallei, a pathogen of significant concern due to its potential for bioterrorism. In Brazil, glanders remains endemic, particularly among working equids in the Northeast region. Diagnostic confirmation typically involves serology, culture, and polymerase chain reaction (PCR), although false-negative PCR results have been increasingly reported. This study aimed to evaluate the diagnostic performance and analytical sensitivity of four B. mallei-specific PCR primer sets using samples from 30 seropositive equids. Microbiological cultures were obtained from various organs and swabs, followed by PCR targeting four genomic regions: fliP-IS407A(a), fliP-IS407A(b), Burk457, and Bm17. All animals were confirmed positive for B. mallei via culture, but PCR detection rates varied significantly across primer sets. The fliP-IS407A(b) primer set showed the highest sensitivity, detecting 86% of samples, while the WOAH-recommended fliP-IS407A(a) set had the lowest performance (13.4%). Analytical sensitivity assays confirmed that fliP-IS407A(b) and Bm17 primers detected DNA concentrations as low as 0.007 ng, outperforming the others. These findings suggest that certain widely used primer sets may lack sufficient sensitivity for reliable detection of B. mallei, especially in chronically infected animals with low bacterial loads. The study underscores the need for ongoing validation of molecular diagnostics to improve the detection and control of glanders in endemic regions.

Background/Objectives: Dental caries remains a prevalent chronic disease globally, driven by complex interactions between the host, diet, and microbial communities. This study employs a metatranscriptomic RNA-Seq analysis to explore the functional dynamics of the dentin microbiome in both healthy and carious teeth. By examining the transcriptional activity of bacterial communities, we aimed to identify key microbial species and molecular functions associated with caries progression. Methods: Samples from six patients (three healthy and three decayed teeth) were analyzed using the Illumina NovaSeq 2000 platform, with data processed through the SAMSA2 pipeline for taxonomic and functional annotation. Results: The differential expression analysis revealed significant upregulation of Streptococcus and Lactobacillus species, including S. mutans, S. sobrinus, and L. salivarius, in carious samples, highlighting their roles in acid production and carbohydrate metabolism. Additionally, Mycobacterium species, known for their biofilm-forming capabilities and acid tolerance, were upregulated in decayed teeth. The Gene Ontology (GO) enrichment analysis identified unique molecular functions and biological processes in carious teeth, such as carbohydrate metabolism, oxidative stress response, and bacterial cell wall biogenesis, which are critical for microbial survival in acidic environments. In contrast, healthy teeth exhibited functions related to homeostasis and nutrient acquisition, reflecting a balanced microbial community. Conclusions: The study underscores the polymicrobial nature of dental caries, with multiple bacterial species contributing to disease progression through diverse metabolic and stress-response mechanisms. These findings provide deeper insights into the ecological shifts within the oral microbiome during caries development, emphasizing the importance of a functional metatranscriptomic analysis in understanding the pathogenesis of dental caries.

In dentistry, various animal models are used to evaluate adhesive systems, dental caries and periodontal diseases. Metalloproteinases (MMPs) are enzymes that degrade collagen in the dentin matrix and are categorized in over 20 different classes. Collagenases and gelatinases are intrinsic constituents of the human dentin organic matrix fibrillar network and are the most abundant MMPs in this tissue. Understanding such enzymes’ action on dentin is important in the development of approaches that could reduce dentin degradation and provide restorative procedures with extended longevity. This in silico study is based on dentistry’s most used animal models and intends to search for the most suitable, evolutionarily close to Homo sapiens. We were able to retrieve 176,077 mammalian MMP sequences from the UniProt database. These sequences were manually curated through a three-step process. After such, the remaining 3178 sequences were aligned in a multifasta file and phylogenetically reconstructed using the maximum likelihood method. Our study inferred that the animal models most evolutionarily related to Homo sapiens were Orcytolagus cuniculus (MMP-1 and MMP-8), Canis lupus (MMP-13), Rattus norvegicus (MMP-2) and Orcytolagus cuniculus (MMP-9). Further research will be needed for the biological validation of our findings.

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has become a major public health worldwide. Hepatic dysfunction has been seen in patients with COVID-19 and could be related to a viral cytopathic effect, an exacerbated immune reaction, or drug-induced liver damage. Currently, routine modification of immunosuppressive therapy in patients with autoimmune hepatitis (AIH) before and after SARS-CoV-2 infection remains an important topic to be discussed. However, there is little evidence about this thematic to support any recommendation. Here, we described a case report in which the use of an immunosuppressive drug by a patient with diagnosed AIH might have influenced the COVID-19 clinical course with altered laboratory hematological and biochemical parameters during infection.

A Lagoa Salgada é um corpo aquático hipersalino costeiro localizado no norte do Estado do Rio de Janeiro e reconhecido pela presença de estromatólitos. As cianobactérias são os principais produtores primários dessas estruturas em lagoas hipersalinas costeiras. O objetivo do estudo foi identificar as cianobactérias presentes na Lagoa Salgada por meio da metagenômica. O material genético obtido de uma amostra de água coletada no mês de junho de 2019 foi submetido ao sequenciamento pelo método shotgun. Os dados metagenômicos foram analisados utilizando o pipeline MetaWrap versão 1.3 para identificação das cianobactérias e dos processos biológicos. O gênero Synechococcus apresentou maior abundância correspondendo por 64,3% das cianobactérias identificadas, seguidos por Synechocystis (23,6%), Geminocystis (2%) e Calothrix (1,8%). As espécies mais abundantes foram Synechococcus sp. RS9909 (46,7%), Synechocystis sp. PCC 6714 (16,4%), Synechococcus sp. WH 8101 (9,2%), Synechocystis sp. CACIAM 05 (4,3%). Foram identificados 33 processos biológicos associados aos genes presentes na amostra. A Lagoa Salgada apresenta uma ampla diversidade de cianobactérias em seu ecossistema aquático ainda pouco explorado, fundamentando a necessidade de proteção e preservação deste ambiente lagunar.

Background: Oral microbiota is considered as the second most complex in the human body and its dysbiosis can be responsible for oral diseases. Interactions between the microorganism communities and the host allow establishing the microbiological proles. Identifying the core microbiome is essential to predicting diseases and changes in environmental behavior from microorganisms. Methods: Projects containing the term “SALIVA”, deposited between 2014 and 2019 were recovered on the MG-RAST portal. Quality (Failed), taxonomic prediction (Unknown and Predicted), species richness (Rarefaction), and species diversity (Alpha) were analyzed according to sequencing approaches (Amplicon sequencing and Shotgun metagenomics). All data were checked for normality and homoscedasticity. Metagenomic projects were compared using the Mann–Whitney U test and Spearman's correlation. Microbiome cores were inferred by Principal Component Analysis. For all statistical tests, p < 0.05 was used. Results: The study was performed with 3 projects, involving 245 Amplicon and 164 Shotgun metagenome datasets. All comparisons of variables, according to the type of sequencing, showed significant differences, except for the Predicted. In Shotgun metagenomics datasets the highest correlation was between Rarefaction and Failed (r = − 0.78) and the lowest between Alpha and Unknown (r = − 0.12). In Amplicon sequencing datasets, the variables Rarefaction and Unknown (r = 0.63) had the highest correlation and the lowest was between Alpha and Predicted (r = − 0.03). Shotgun metagenomics datasets showed a greater number of genera than Amplicon. Propionibacterium, Lactobacillus, and Prevotella were the most representative genera in Amplicon sequencing. In Shotgun metagenomics, the most representative genera were Escherichia, Chitinophaga, and Acinetobacter. Conclusions: Core of the salivary microbiome and genera diversity are dependent on the sequencing approaches. Available data suggest that Shotgun metagenomics and Amplicon sequencing have similar sensitivities to detect the taxonomic level investigated, although Shotgun metagenomics allows a deeper analysis of the microorganism diversity. Microbiome studies must consider characteristics and limitations of the sequencing approaches. Were identified 20 genera in the core of saliva microbiome, regardless of the health condition of the host. Some bacteria of the core need further study to better understand their role in the oral cavity.