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Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot
<h4>Objectives</h4>Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history …
Read PDFMetagenomic biodiversity assessment within an offshore wind farm
Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and …
Read PDFGut-Heart Axis in Myocardial Repair: Mechanisms, Cross-Organ Networks, and Therapeutic Opportunities
Cardiovascular diseases remain the leading global cause of morbidity and mortality, placing an escalating burden on health care systems and economies. While the gut microbiota is well recognized in atherosclerosis and cardiometabolic disorders, its influence …
Read PDFComparative metagenomic analysis of bacterial and fungal communities associated with bayoud-resistant and susceptible date palm cultivars in the Zagora oasis-Morocco
BACKGROUND: Fusarium oxysporum f. sp. albedinis (Foa) is a destructive soil-borne fungal pathogen responsible for bayoud disease, which threatens date palm cultivation in North Africa. This disease has caused significant agricultural losses, particularly in Morocco, …
Read PDFLactobacillus-Dominated Cervical Microbiota Revealed by Long-Read 16S rRNA Sequencing: A Greek Pilot Study
<b>Background/Objectives:</b> The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function …
Read PDFGut microbial diversity impacts carbohydrate fermentation by children with severe acute malnutrition
African children suffering from severe acute malnutrition (SAM) have a disrupted gut microbiome and low short-chain fatty acids (SCFAs). These are linked to persistently high mortality and morbidity rates. Supplementing recovery feeding regimes with suitable …
Read PDFRed Complex Bacteria as a Hidden Cause of Chronic Lung Abscess: A Case Report
BACKGROUND Common oral pathogens such as Treponema denticola, Porphyromonas gingivalis, and Tannerella forsythia, which form biofilms in the periodontal pockets, are classified together as Red Complex bacteria in Socransky's subgingival cluster model and are key …
Read PDFStewarding the hospital sink drain: a narrative review of practical approaches for controlling gram negative pathogens in low- and middle-income countries
In low- and middle-income countries (LMICs), gram-negative bacteria cause over half of intensive care unit (ICU) infections, with up to 50% mortality associated with multidrug-resistant (MDR) strains. Hospital sink drains are increasingly recognized as reservoirs …
Read PDFIntegrated genomics, metagenomics and metatranscriptomics to reveal the biocontrol mechanism of <i>Bacillus velezensis</i> JY10 against tobacco target spot disease
Tobacco target spot (TTS) disease, a prevalent fungal disease caused by <i>Rhizoctonia solani</i>, severely reduces tobacco yield and quality, imposing substantial economic losses on the tobacco industry. In this study, we employed a biological control …
Read PDFAltered SIgA-targeting of gut microbiota is associated with long-term dysbiosis in pediatric solid organ transplant recipients
The composition of the gut microbiota (GM) is altered in solid organ transplantation (SOT) recipients, where the degree of dysbiosis is associated with long-term survival and is believed to be influenced by immunosuppression therapy. At …
Read PDFWhat are we eating?. Detection of antibiotic resistance mechanisms in frozen chicken nuggets imported from Brazil
The rise of antibiotic resistance is a growing challenge, affecting humans, the environment, and animals. Under the One Health framework, this study investigated resistance mechanisms to critically important antibiotics in frozen chicken nuggets imported from …
Read PDFSynthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture
Climate change poses significant threats to global agricultural productivity, necessitating innovative strategies to ensure food security and ecological sustainability. One promising avenue lies in the deliberate design and deployment of synthetic microbiomes and engineered rhizospheres …
Read PDFThe crayfish-rice coculture model contributes to regulating the soil fertility of rice fields and maintaining the stability of soil microbial community composition and function
Rice-fish coculture represents a classic sustainable agricultural paradigm; however, the microecological mechanisms underlying its capacity to maintain soil fertility and microbial community stability remain poorly understood. We conducted a 13-month field experiment comparing three cultivation …
Read PDFA hidden confounder for microbiome studies: medications used years before sample collection
Medication usage is a known contributor to the inter-individual variability of the gut microbiome. However, medications are often used repeatedly and for long periods, a notion yet unaccounted for in microbiome studies. Recently, we and …
Read PDFAdvances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning
Molecular profiling enabled by meta-omics technologies has significantly expanded our knowledge of microbial catalog across diverse environments. Increasing attention has now been focused on identifying ecologically significant taxa, particularly keystone that stabilize communities, rare taxa …
Read PDFPredicting coarse-grained representations of biogeochemical cycles from metabarcoding data
<h4>Motivation</h4>Taxonomic analysis of environmental microbial communities is now routinely performed thanks to advances in DNA sequencing. Determining the role of these communities in global biogeochemical cycles requires the identification of their metabolic functions, such as …
Read PDFBibliometric analysis of the application of artificial intelligence techniques in bacteriology: a PRISMA-guided research agenda
<h4>Introduction</h4>The integration of artificial intelligence (AI) into bacteriology has marked a pivotal advancement by enabling the analysis of large-scale microbiological datasets. Despite growing adoption, significant research gaps persist, hindering the full exploitation of AI's potential …
Read PDFMachine learning approach and internet of things technologies to unravel the complex interaction between microbiome-metabolome in inflammatory bowel disease: a new frontier in precision medicine
Inflammatory bowel diseases (IBD) are chronic, relapsing inflammatory disorders with ulcerative colitis (UC) and Crohns disease (CD) representing the two major phenotypes. While these conditions share common features, they exhibit distinct clinical presentations, disease behaviors, …
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