Search the literature by keyword, topic, or author. Filter to articles with full text available.
1201 results
Ice caves constitute one of the last cryospheric environments studied in the meridional regions. They are undergoing a pronounced ice reduction, and are an important example of ecosystems that have not yet been thoroughly explored …
Read PDFDue to an insufficient understanding of the dynamic mechanisms underlying seasonal variations in Daqu fermentation quality, such as microbial community succession, enzyme activity, and metabolic regulation, precise control of Daqu quality and consistency across different …
Read PDFThe skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader …
Read PDFBACKGROUND: Livestock production contributes to the emergence and spread of antimicrobial resistance (AMR), with pig farming accounting for a large share of veterinary antibiotic use. Manure application to fields can release drug-resistant bacteria and AMR …
Read PDFWe present an open-source QIIME2 pipeline for 16S multi-amplicon sequencing. Benchmarked against proprietary software with a mock community, our workflow demonstrates comparable sequencing depth and taxonomic accuracy (F1-Score=0.875). The multi-region approach outperforms single amplicons, validating …
Read PDFReproducible microbiome profiling is essential for linking microbial communities to host health, yet methodological variation continues to undermine reproducibility across studies. This problem is acute in pig microbiome research, where no standardized DNA extraction protocols …
Read PDFThrough the selective breeding of superior strains, livestock and poultry can achieve enhanced disease resistance and production performance, thereby improving farming efficiency and increasing chicken meat yield. This study analyzed the expression of gut health-related …
Read PDFDNA contigs binning is necessary to reconstruct metagenome-assembled genomes. Current metagenomic DNA contigs binning methods often leverage coverage profiles across multiple related metagenomes and have demonstrated strong performance on co-assembled contigs. However, in single-sample scenarios …
Read PDF<h4>Introduction</h4>Bats play important ecological roles but can also harbor a wide diversity of pathogens, including trypanosomatids. Knowledge about the circulation of Trypanosoma spp. in bat ectoparasites remains limited, particularly in peri-urban environments.<h4>Methods</h4>In this study, we …
Read PDFThe vast majority of microorganisms in the environment remain uncultured using conventional laboratory techniques, representing an immense untapped reservoir of genetic and chemical diversity. Recent innovations in cultivation strategies, combined with advances in metagenomics, single-cell …
Read PDF<h4>Background & aims</h4>The THEMATIC trial demonstrated that fecal microbiota transplantation (FMT) reduces recurrence of hepatic encephalopathy (HE) in patients already receiving lactulose and rifaximin. The aim of this analysis was to identify multi-omic predictors of …
Read PDFOncogenic viruses cause high-risk cancers in humans and are responsible for nearly 20% of all cancer cases worldwide. Currently, very limited data exist in the realm of wastewater-based viral epidemiology (WBE) for cancer-causing viruses, with …
Read PDFReintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this …
Read PDFAutism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. …
Read PDFAncient metagenomic studies using capture or shotgun sequencing often perform pairwise alignment of individual reads against large reference databases followed by lowest common ancestor assignment for taxonomic identification. Here, we present bamdam, a lightweight post-mapping, …
Read PDFEllagitannins and ellagic acid are microbially converted into urolithins, metabolites associated with antioxidant, anti-inflammatory, and mitochondrial-related activities. Although several human-derived urolithin-producing strains and their associated enzymes have recently been characterised, the diversity of microbial strategies …
Read PDF<i>Inonotus hispidus</i> is a medicinal fungus that grows on <i>Morus alba</i> L., <i>Fraxinus mandshurica</i> Rupr., and <i>Ziziphus jujuba</i> Mill. However, there have been no reports on the comparative study of microbial diversity and metabolites in …
Read PDFHighland barley Baijiu is a kind of fermented liquor with national characteristics produced in the Qinghai-Tibet Plateau, and its quality largely depends on the highland barley Baijiu Daqu (HBQ). HBQ contains abundant microbial resources and …
Read PDFAutism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, …
Read PDFAs the most abundant biological entities in the ocean, viruses of microbes play important roles in regulating host population dynamics and influencing biogeochemical cycles. Metagenomic surveys have revealed an astounding reservoir of viral genetic diversity …
Read PDF