Tag Archives: nutrition

December 19, 2025

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Animal microbiome

The innate immune IMD pathway is a key regulator of gut microbiome and metabolic homeostasis in the black tiger shrimp (Penaeus monodon) – Premruethai Supungul – PLOS ONE

Human gut microbiome & nutrition

The evaluation of indoxyl sulfate in the general population in Kanegasaki Iwate: A cross-sectional study (KANEGASAKI study) – Mizuki Hisano – PLOS ONE

The relationship between dietary intake of B vitamins and Helicobacter pylori seropositivity – Yuexia Lu – PLOS ONE

Plant, soil & ecological microbiome

Zinc ion increases the effectiveness of phosphorus in agricultural soils through microbial solubilization – Lanxin Tang – PLOS ONE

Optimizing soil quality and rhizosphere ecology to enhance Annona squamosa yield and quality through water–fertilizer–mulching synergy – Weihua Wang – PLOS ONE

Concentration-dependent effects of fermented spent coffee grounds and contrasting effects of earthworms on growth and phytochemicals in medicinal plant Glechoma longituba – Bing-Nan Zhao – PLOS ONE

Animal experiments (model organisms)

The Drosophila G protein-coupled receptor, GulpR, is essential for lipid mobilization in response to nutrient limitation – Daniela Barraza – PLOS Genetics

High-protein diets reduce plasma pro-inflammatory cytokines following lipopolysaccharide challenge in Swiss Albino mice – Hellen W Kinyi – PLOS ONE

Clinical research & public health

Impact of an integrated intervention package during preconception, pregnancy, and early childhood on inflammation, IGF-1, IGFBP3 during first 6 months of life: Findings from the WINGS randomized controlled trial – Ranadip Chowdhury – PLOS Global Public Health

Lack of association between loneliness, social isolation and inflammation in people living with HIV aged ≥50 years – Jose-Ramon Blanco – PLOS ONE

Effect of obesity and exercise training on circulating lipids in American Indian adolescents – Charles F Hojjat – PLOS ONE

From mental health detention to health systems reform: Co-producing policy and practice recommendations with Black men and their communities – Elaine Craig – PLOS Mental Health

Microbial genetics & bacterial physiology

Whole-genome analysis of Lysinibacillus boronitolerans MSR1: A dairy-isolated multidrug-resistant and non-pathogenic strain – Md Shahedur Rahman – PLOS ONE

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and intra-species cooperation – Ben Vezina – PLOS Biology

Clinical biomarkers & immunology

Blood RNA biomarkers and a point-of-care elastase assay for detecting host immune activation in suspected sepsis – John E Lafleur – PLOS ONE

Multi-omics analysis reveals diagnostic and therapeutic biomarkers for aging phenotypes in ulcerative colitis – Lei Guo – PLOS ONE

Oral health & microbiome

The impact of diet and oral hygiene on dental caries among Turkish children: A cross-sectional study – Ozge Yesildemir – PLOS ONE

Molecular biology & immunity

LIPL-1 and LIPL-2 are TCER-1-regulated lysosomal lipases with distinct roles in immunity and fertility – Laura Bahr – PLOS Genetics

October 17, 2025

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Gut Microbiome & Health

Lactic acid produced by optimal vaginal Lactobacillus spp. potently and specifically inactivates HIV-1 in vitro by targeting the viral RNA genome and reverse transcriptase
– Muriel Aldunate – PLOS Pathogens

Differential composition of the pulmonary microbiome in HIV-positive versus HIV-negative patients with Pneumocystis jirovecii
– Chang-Run Zhang – PLOS ONE

Risk of atopic dermatitis in periodontitis patients with and without dental scaling: A retrospective cohort study
– Ming-Che Chiang – PLOS ONE

Fecal carriage and associated factors of extended-spectrum beta-lactamase-producing Enterobacteriaceae in children under five years old with diarrhea at a tertiary hospital in Tanzania
– Emily M. Jackson – PLOS ONE

Pathogens, Immunity & Host Interactions

Dietary tannic acid promotes intestinal clearance of Candida albicans by cross-linking hyphal chitosan
– Jia Feng – PLOS Pathogens

Trends in Clostridioides difficile infection prevalence among pediatric cancer patients: A systematic review and meta-analysis
– Muluneh Assefa – PLOS ONE

Multiplex serology for Streptobacillus moniliformis and other ‘rat bite fever-like’ microorganisms for seroprevalence studies in rodents
– Katja Schmidt – PLOS ONE

Animal & Environmental Microbiomes

Effects of rumen-protected or unprotected Clostridium butyricum on growth performance, rumen fermentation, immunity and antioxidation in fattening goats
– Caixia Zhang – PLOS ONE

The intracellular symbiont Wolbachia alters Drosophila development and metabolism to buffer against nutritional stress
– Amelia R. I. Lindsey – PLOS Genetics

Interactive effects of developmental and adult nutrition on lifespan and fecundity in a genetically diverse Drosophila population
– Andrew Jones – PLOS ONE

Metabolism, Health & Disease

Alterations in the serum metabolome in patients with the COVID-19 Omicron variant and in recovered cases
– Feng Gao – PLOS ONE

Humanized monoacylglycerol acyltransferase 2 mice on a high-fat diet exhibit impaired liver detoxification during metabolic dysfunction-associated steatotic liver disease
– J. Jose Corbalan – PLOS ONE

Current and future burden of gynecological cancers attributable to high body-mass index: A comprehensive global analysis and projection study
– Xuanyu Zhao – PLOS ONE

Developing and experimentally validating a glucocorticoid signaling-related gene signature to evaluate the prognosis and immunotherapeutic response in kidney renal clear cell carcinoma
– Yu Zhang – PLOS ONE

Computational & Bioinformatics Advances

ArcDFI: Attention regularization guided by CYP450 interactions for predicting drug–food interactions
– Mogan Gim – PLOS Computational Biology

Advanced deep learning-based brain tumor classification using a novel customized CNN and optimized residual network
– Mehwish Rasheed – PLOS ONE

June 19, 2024

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Oral and respiratory microbiota

Safety, Feasibility, and Advantages of Oral Microbiota Transplantation: The First Clinical Case – Oleg V. Goloschapov – Journal of Pediatric Hematology/Oncology

Oral microbial dysbiosis in patients with oral cavity cancers – Ozge Unlu – Clinical Oral Investigations

Nasal cathelicidin is expressed in early life and is increased during mild, but not severe respiratory syncytial virus infection – Sofia Sintoris – Nature Scientific Reports

Human gut microbiome

Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges – Lucas Masier – Nature Metabolism

Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice – Yohannes Seyoum – Nature Communications

Beneficial microbes and compounds

Short-chain fatty acid valerate reduces voluntary alcohol intake in male mice – Suresh C. Bokoliya – BMC Microbiome

Sleep promoting and omics exploration on probiotics fermented Gastrodia elata Blume – Chao-Qi Zhang – NPJ Science of Food

Animal microbiome

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human – Li Tian – BMC Microbiome

Water and extremophile microbiome

Bacterial community and cyanotoxin gene distribution of the Winam Gulf, Lake Victoria, Kenya – Katelyn M. Brown – Environmental Microbiology

Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water – Nataliya Teteneva – ISME Journal

Plant, root, and soil microbiomes

Root-associated Streptomyces produce galbonolides to modulate plant immunity and promote rhizosphere colonization – Clément Nicolle – ISME Journal

Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome – Zi-Teng Liu – Nature Communications

Conceptualizing soil fauna effects on labile and stabilized soil organic matter – Gerrit Angst – Nature Communications

Fungi

The first ITS1 profiling of honey samples from the Southeast Asian region Lombok, Bali and Banggi Island – Saeed Ullah – Nature Scientific Reports

Archaea

Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery – Biyan Huang – ISME Journal

Microbial Ecology

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution – Hagay Enav – Nature Biotechnology

Methods

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding – Karl D. Gaisser – Nature Protocols

Commentary and opinions

SeqCode in the golden age of prokaryotic systematics – Diego Javier Jiménez – ISME Journal

Digestive Disease Week 2024 – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Barriers and enablers to the effective implementation of omics research in low- and middle-income countries – Jacus S. Nacis – Nature Biotechnology

April 10, 2024

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Good morning microbiome enthusiasts! Today’s MD is on the shorter side but we still have some really interesting articles picked out for you to peruse – including a microbiome-sparing targeted P. aeruginosa compound, effective probiotics for restoring a healthy coral microbiome, and a study characterizing the microbiome of metastatic cancers in over 4,000 biopsies. Plus, don’t forget that April’s Microbiome Virtual International Forum is happening next week!

Human Microbiome

Longitudinal multi-omics analysis uncovers the altered landscape of gut microbiota and plasma metabolome in response to high altitude – Yang Han et al – BMC Microbiome

Illuminating microflora: shedding light on the potential of blue light to modulate the cutaneous microbiome – Hannah J Serrage et al – Frontiers in Cellular and Infection Microbiology

Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC – Rauf Salamzade et al – Microbial Genomics

A pan-cancer analysis of the microbiome in metastatic cancer – Thomas Battaglia et al – Cell

A Lacticaseibacillus rhamnosus secretome induces immunoregulatory transcriptional, functional and immunometabolic signatures in human THP-1 monocytes – Michael P. Jeffrey et al – Nature Scientific Reports

The oral cavity and intestinal microbiome in children with functional constipation – Monika Kwiatkowska et al – Nature Scientific Reports

Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults – Casper S. Poulsen et al – Nature Scientific Reports

Colonization during a key developmental window reveals microbiota-dependent shifts in growth and immunity during undernutrition – Yadeliz A. Serrano Matos et al – BMC Microbiome

Animal models

Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice – Tatsuya Dokoshi et al – Nature Communications

A folate inhibitor exploits metabolic differences in Pseudomonas aeruginosa for narrow-spectrum targeting – Connor Chain et al – Nature Microbiology

Animal microbiome

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience – Lauren F. Messer et al – Nature Communications

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment – Nathalia Delgadillo-Ordoñez et al – Nature Communications Biology

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation – Daxi Wang et al – BMC Microbiome

Plant, root & soil microbiome

Root volatiles manipulate bacterial biofilms – Waseem Raza & Gaofei Jiang – Nature Ecology & Evolution

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community – Chong-Die Wu et al – BMC Plant Biology

Bioinformatics & tools

Holomics – a user-friendly R shiny application for multi-omics data integration and analysis – Katharina Munk et al – BMC Bioinformatics