Latest Articles

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  Section: Microbiology ; Topics: Microbiology, Environmental sciences, Genetics/genomics

  Comparing DNA extraction protocols for freshwater prokaryotic communities: impacts on yield and microbial profiling

  Szylit, Arthur;   Jardillier, Ludwig;   Ciobanu, Maria-Cristina;   Cabrol, Léa;   Barret, Maialen;   Christaki, Urania  

  10.24072/pcjournal.788 - Peer Community Journal, Volume 6 (2026), article no. e93

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  DNA extraction from aquatic samples is a critical process that influences the quantity and purity of the DNA obtained. This can have profound effects on the accuracy of the community depiction. In this study, DNA extraction workflows of seven commercial kits (Qiagen: DNeasy PowerLyzer PowerSoil, DNeasy PowerSoil Pro, DNeasy PowerSoil, DNeasy PowerMax Soil; Macherey-Nagel: NucleoSpin Soil; Zymo: ZymoBIOMICS DNA; MP Biomedicals: FastDNA SPIN), along with several modifications of manufacturer’s protocols focusing on the lysis and elution steps, were tested, accounting for a total of 18 different protocols. For each protocol, DNA yield (quantity, replicability and quality), richness and compositional reproducibility based on 16S rRNA gene sequencing, as well as processing time and cost were assessed. The standard protocols recommended by the manufacturer showed comparable DNA yield results. Shared ASVs between all protocols accounted for >90% of the reads and were mostly abundant ASVs, indicating consistent detection of dominant taxa across all protocols. Adding supplementary lysis and elution steps to the manufacturer's protocols yielded up to ~4× more DNA. However, total read counts and ASV richness were lower as total DNA increased. Manufacturer’s protocols therefore showed higher values than their modified versions, although these effects were not significant on community composition. We conclude that the choice of a protocol is the balance between recovering sufficient DNA of good quality versus potential effects on downstream sequencing output (reads and ASVs).

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  Section: Microbiology ; Topics: Microbiology

  Monoclonal anti-dsRNA antibody-based metagenomics (MADAM) reveal Pyricularia oryzae mycovirome

  Blondin, Laurence;   Filloux, Denis;   Fernandez, Emmanuel; Adreit, Henri; Huang, Huichuan;   Fournier, Elisabeth;   Tharreau, Didier;   Roumagnac, Philippe  

  10.24072/pcjournal.782 - Peer Community Journal, Volume 6 (2026), article no. e92

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  This study introduces MADAM (Monoclonal Anti-dsRNA Antibody-Based Metagenomics), a novel approach that integrates multiple technical modules previously used independently in other protocols. MADAM combines monoclonal antibody-mediated double-stranded RNA (dsRNA) enrichment, sequence-independent RT-PCR, and Oxford Nanopore Technologies (ONT) sequencing. Applied to Pyricularia oryzae, the causal agent of rice blast disease, MADAM enabled the comprehensive characterization of mycovirus genomes from four fungal isolates collected in Yunnan, China. The approach achieved high viral read recovery rates (46.9-72.7%) and identified 18 P. oryzae-associated RNA viruses spanning seven families: Botourmiaviridae, Deltaormycoviridae, Mymonaviridae, Partitiviridae, Polymycoviridae, Splipalmiviridae, and Ambiguiviridae. Seventeen nearly complete to complete viral genomes (1,226-6,085 nucleotides) were recovered, with sequence coverage ranging from 88% to 100%. Co-infections were detected in three of the four isolates, with notable discoveries including the first deltaormycovirus reported in P. oryzae, a putative novel member of Botourmiaviridae, and an additional genomic segment of a polymycovirus. MADAM successfully detected positive-sense, negative-sense ssRNA, and dsRNA viruses, demonstrating its broad applicability. By uncovering novel viruses and resolving complex co-infections, this method proves invaluable for fungal virology, with potential applications in diagnostics, surveillance, and biological control. Ultimately, MADAM advances our understanding of fungal viral diversity and paves the way for further exploration of mycovirus ecology and evolution.

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  Section: Health & Movement Sciences ; Topics: Physiology

  Postprandial Triglyceride Excursions and the Potential Effect of Menstrual Cycle Phases: A Narrative Review of Human Physiology with Clinician and Patient Perspectives

  Goulet, Nicholas;   Lyndon, Sydney; Bohlen, Alice; Antunes, Paulo; Beaudry, Nicole; Imbeault, Pascal  

  10.24072/pcjournal.777 - Peer Community Journal, Volume 6 (2026), article no. e91

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  Postprandial lipemia, the transient rise in circulating triglyceride-rich lipoproteins after consuming a meal, plays a significant role in cardiometabolic disease risk beyond the contribution of fasting lipid concentrations. While pharmaceutical therapies have been highly effective in reducing fasting cholesterol and fasting lipids, strategies to lower postprandial triglyceride excursions remain limited. Further, females have historically been underrepresented in research, partially due to concerns about hormonal variability across the menstrual cycle. Yet, understanding how menstrual cycle phases influence postprandial triglyceride metabolism is essential for designing inclusive studies and refining clinical approaches to reduce cardiovascular disease risk. This narrative review synthesizes current evidence on postprandial triglyceride metabolism, biological sex-related differences, hormonal fluctuations across the menstrual cycle phases, and potential menstrual cycle influences on postprandial triglyceride metabolism. Premenopausal females generally display lower postprandial triglyceride excursions than males, driven primarily by accelerated clearance of triglyceride-rich lipoproteins through enhanced skeletal muscle uptake and shorter particle residence times. The influence of menstrual cycle phase on postprandial triglyceride excursions remains unresolved. Of four known studies conducted to date, two reported no phase-dependent differences, and two observed lower triglyceride concentrations in the luteal phase. This heterogeneity may reflect methodological variability rather than a consistent biological effect. Nevertheless, mechanistic evidence linking estrogen and progesterone to hepatic lipoprotein production and tissue lipid handling provides biological plausibility for menstrual cycle modulation of postprandial lipemia and underscores the need for more rigorously designed studies with biochemical hormonal verification. Complementary perspectives from a community clinician and a patient partner are included to provide insights into the practical implications of postprandial lipemia for patient care and the lived experiences of cardiometabolic disease prevention.

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  Section: Microbiology ; Topics: Microbiology, Sustainability science

  A newly identified Comamonas serinivorans strain for PHA production from sterile-filtered dark-fermentation-derived volatile fatty acids: isolation, metabolic profiling and industrial prospects.

  Gautier, Kelvin; Pattyn, Pauline; Briki, Amani;   Soric, Audrey;   Irague, Romain  

  10.24072/pcjournal.785 - Peer Community Journal, Volume 6 (2026), article no. e90

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  Dark-fermentation for hydrogen production leaves a substantial fraction of substrate carbon unexploited, with a large fraction remaining as volatile fatty acids (VFAs), mainly acetate and butyrate. To improve process valorisation, this study investigates the microbial conversion of fermentation-derived VFAs into polyhydroxyalkanoates (PHAs). A PHA-producing strain was isolated from dairy wastewater sludge using a feast-famine enrichment strategy and identified as Comamonas serinivorans ATH based on 16S rRNA gene sequencing. The strain exhibited strict specialisation towards organic acids, efficiently assimilating VFAs but not carbohydrates. Under nutrient limitation, intracellular PHA accumulation reached up to 93% of cell dry weight. When cultivated in a sterile-filtered dark-fermentation stream, the strain consumed both acetate and butyrate and produced PHA with a yield of 0.54 g/g of consumed VFAs under non-optimised conditions. GC-MS analysis confirmed that Comamonas serinivorans ATH produces a polymer mainly composed of 3-hydroxybutyrate monomers. These findings demonstrate the feasibility of coupling hydrogen-producing dark-fermentation with PHA synthesis, supporting an integrated biorefinery approach for sustainable bioplastic production from waste-derived carbon streams.