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Microbiome Digest - Bik's Picks | A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigestA daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigestMicrobiome Digest - Bik's Picks | A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest Microbiome Digest – Bik's Picks A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest Menu Skip to content HomeFun stuff I Could Not Resist – Bik’s Brain Journal Clubs Lab Stock Photo Fails Microbiome Collection Fungi / Mycobiome General Microbiome Reviews Human Microbiome Paper Collection Human Armpit and Belly button Microbiome Human Beard Microbiome Human Breast Milk Microbiome Human Gut Microbiome Human Oral Microbiome Human Respiratory Microbiome Human Skin Microbiome Human Stomach Microbiome Human Vaginal Microbiome Infant colonization Microbiome and the influence of sex Pregnancy microbiome Probiotics papers Wound microbes Microbiome Blogs, Tweeps, and Books Microbiome Techniques Bioinformatics tools paper collection Contamination issues Extraction and Amplification Sample storage Non-Human Microbiome Paper Collection Animal microbiome Archaeological Microbiology Beer and Wine Microbiology Built Environment Microbiome Culture collections Food Making Microbiology Forensic Microbiology Microbes in space Microbiology of Probiotics Microbiome Of Death Microbiome Vocabulary Microbiome, speciation, evolution Outdoor Air, Rain, Snow Microbiome Plant, Root, and Soil Microbiome Synthetic microbial communities Water Microbiome Virome papers Microbiome News Articles Collection Our Bodies’ Best Buddies About Microbiome Digest About the team Elisabeth Bik Expert Women in Microbiology Our search alerts Post navigation ← Older posts October 6, 2024 Posted on October 6, 2024 by JP Cardenas Human and General Microbiome Noninvasive, microbiome-based diagnosis of inflammatory bowel disease – Jiaying Zheng – Nature Medicine Advancing microbiome research in Māori populations: insights from recent literature exploring the gut microbiomes of underrepresented and Indigenous peoples – Ella T Silk – mSystems Salivary microbiota reflecting changes in subgingival microbiota – Jae-Suk Jung – Microbiology Spectrum Differences in the human gut microbiota with varying depressive symptom severity scores – Yuka Masamura – Bioscience of Microbiota, Food and Health Review: Sophorolipid: An Effective Biomolecule for Targeting Microbial Biofilms – Sunidhi Dhadwal – Current Microbiology News: Microbiome-based treatment helps ease severe malnutrition – Elizabeth Pennisi – Science Beneficial Microbes and Compounds A multivalent mRNA-LNP vaccine protects against Clostridioides difficile infection – Mohamad-Gabriel Alameh – Science Safety and Tolerability of CP101, a full spectrum, oral microbiome therapeutic for the prevention of recurrent C. difficile infection: A Phase 2 Randomized Controlled Trial – Jessica R Allegretti – Gastroenterology Animal Microbiome Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection – María Dolores Ramos-Barbero – The ISME Journal Structural and functional differences of gut microbiota in Pomacea canaliculata from different geographical locations and habitats – Miao Fang – Ecology and Evolution Plant Microbiome Rhizosphere microbial community structure in high-producing, low-input switchgrass families – Christina Stonoha-Arther – PloS One Dynamic alterations and ecological implications of rice rhizosphere bacterial communities induced by an insect-transmitted reovirus across space and time – Nan Wu – Microbiome Microbiome Analysis: Tools, Techniques and Resources  Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing – Zihe Xu – Cell Reports rRNA operon improves species-level classification of bacteria and microbial community analysis compared to 16S rRNA – Sohyoung Won – Microbiology Spectrum ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies – Andrea Fasolo – PloS One Posted in General Microbiome, Human gut, Uncategorized | Tagged Animal microbiome, animal models, human microbiome, microbiome, microbiome analysis, Microbiome Digest, Plant microbiome | Leave a comment October 4, 2024 Posted on October 3, 2024 by Svetlana Ugarcina Perovic Happy Friday! And see you next week at MVIF! Exciting lineup for #MVIF 32!⭐️MicroTalks:🇰🇷Nayeon Kim (Lee & @BelenkyLab)🇯🇵Hirotsugu Shiroma (@takujida)⭐️Keynote: 🇺🇸 Susan Bullman @BullmanLab⭐️Selected talks:🇺🇸@laurenmlui🇺🇸@jsung0906🇸🇬@aarthiravikrishHot Topics: 🐭, Enteropathway database, Nanopore seq & more! pic.twitter.com/4MDF4xzk8E— Microbiome Virtual International Forum (@MicrobiomeVIF) October 1, 2024 Plastisphere microbiome What harmful microbes are lurking in the world’s 7 billion tonnes of plastic waste? – Changchao Li – NatureRespiratory microbiome Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis – Hongbin Chen – npj Biofilms and Microbiomes Vaginal microbiome Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples – Hayden N Brochu – bioRxiv Oral microbiome The intensive physical activity causes changes in the composition of gut and oral microbiota – Szymon Urban – Scientific Reports “Twenty professional football players and twelve amateurs were invited to the study groups.” Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome – Yuya Kiguchi – bioRxiv Excited to share our new preprint!We identified a novel extrachromosomal element, named "Inocle," in the human oral microbiome. Inocles are giant (max 395kb) and surprisingly found in 74% of the worldwide population.https://t.co/6a4vHUy26r— Yuya Kiguchi, PhD (@nu1chan) October 1, 2024 The association between mode of childbirth delivery and early childhood caries: A comprehensive systematic review and meta-analysis – Li Xiang – PlosOne Gut microbiome What’s GABA got to do with it? A potential link between the microbiome, schizophrenia, and the endo-cannabinoid system – Ayala Glinert – Psychiatry Research Changes in intestinal permeability and gut microbiota following diet-induced weight loss in patients with metabolic dysfunction-associated steatohepatitis and liver fibrosis – Dimitrios A. Koutoukidis – Gut Microbes Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis – Yan Jia – Scientific Reports Detailed Analysis of Prebiotic Fructo- and Galacto-Oligosaccharides in the Human Small Intestine – Mara P. H. van Trijp – Journal of Agricultural and Food Chemistry Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape – Erica T. Grant – Microbiome Human milk microbiome Maternal HIV infection and the milk microbiome – Nicole H. Tobin – Microbiome Viruses and phages Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens – Mihály Koncz – Cell 📢 Thrilled to announce our latest research in @CellCellPress! We've created a global ‘superbug map’ for a critically antibiotic-resistant bacterium to inform #phagetherapy 🧵1/11 https://t.co/TVAzlSOxIx pic.twitter.com/ChvLlnVLs2— BalintKintsesLab (@KintsesLab) September 27, 2024 Animals Differential interactions of Rickettsia species with tick microbiota in Rh. sanguineus and Rh. turanicus – Apolline Maitre – Scientific Reports  Animal experiments Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer – Rachel C. Fellows – Science Advances Exciting new work from my lab looking at how the circadian clock governs the gut microbiome composition and intestinal barrier function during colorectal cancer progression! @UCIMedSchool @UCIrvine https://t.co/FlABnuApa1— Selma Masri (@masrilab) September 30, 2024 Photoperiod effects on corticosterone and seasonal clocks in cafeteria-induced obese fischer 344 rats are influenced by gut microbiota – Verónica Arreaza-Gil – Scientific Reports  🔽 How does the interaction between photoperiods and gut microbiota affect corticosterone? I am delighted to share the last article of my thesis in collaboration with @harschellekens. Congratulations to all the co-authors!! @cristinatorfue @AnnaArolaArnal https://t.co/ergZY2FE82— Verónica Arreaza Gil (@varreazagil) September 30, 2024 Plant, root, soil microbiome Closing the gap: examining the impact of source habitat proximity on plant and soil microbial communities in post-mining spoil heap succession – Lenka Mészárošová – Frontiers in Microbiology Bacterial Communities from the Antique Roman City of Carnuntum (Austria):16S r-RNA-Based Comparison of Soil Samples from Different Archaeological Horizons – Johann Michael Köhler – preprints Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient – Viviana Freire-Zapata – Nature Microbiology Phosphorus availability influences disease-suppressive soil microbiome through plant-microbe interactions – Yifan Cao – Microbiome Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils – Luiz A. Domeignoz-Horta – Nature Communications Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest – Madison Goforth – Plos One Drinking water microbiomeMaking waves: From tap to gut- exploring the impact of drinking water on gut microbiota – Hanieh Shakeri Moghaddam – Water Research Bioinformatics Taxometer: Improving taxonomic classification of metagenomics contigs – Svetlana Kutuzova – Nature Communications Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences – Yasas Wijesekara – bioRxiv After three years of hard work, I’m thrilled to share the brainchild of my PhD project.Jaeger: a deep learning tool for identifying bacteriophage sequences in metagenomes! 🧬🦠 Empowering exploration of the viral world with greater accuracy and insight.https://t.co/xdsCOHvJKV— Yasas Wijesekara (@RajithaYasas1) October 1, 2024 Emergent ecological patterns and modelling of gut microbiomes in health and in disease – Jacopo Pasqualini – Plos Computational Biology Technique Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing – Harry T. Child – Access Microbiology Microbial community interactions on a chip – Duane S. Juang – PNAS BIG thanks to everyone involved in the #PooSticksStudy! 🦠🧬💊Here’s what we’ve achieved together from 1 June to 30 September 2024:➡️1,530 people expressed interest in joining 🙌➡️729 volunteers were eligible to take part (393 swimmers 🏊‍♀️& 336 non-swimmers )➡️624… pic.twitter.com/DwmofYP1cp— Elitsa Penkova 🦠 (@PenkovaElitsa) October 1, 2024 Posted in Animal experiments, Animal microbiome, Events and jobs, Fecal Transplants, Food Microbiology, General Microbiome, Human gut, Human oral, Human reproductive or urinary, Human respiratory, Metagenomics & Bioinformatics, Microbial Ecology, Phages and viruses, Plant Root Soil microbiome, Pregnancy and birth, Techniques, Water microbiome | Leave a comment October 2, 2024 Posted on October 2, 2024 by Grace Deitzler Gut Microbiome Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants – Brandon Hickman et al – Nature Communications Pangenomes of human gut microbiota uncover links between genetic diversity and stress response – Saar Shoer et al – Cell Host & Microbe [MINI REVIEW] The human gut microbiome in health and disease: time for a new chapter? – Jee-Yon Lee et al – ASM Infection & Immunity Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities – Amin Valiei et al – NPJ Biofilms & Microbiomes A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases – Wen Sun et al – NPJ Biofilms & Microbiomes A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome – Tetsuro Kawano-Sugaya et al – BMC Microbiome Stratification of human gut microbiomes by succinotype is associated with inflammatory bowel disease status – Laura Anthamatten et al – BMC Microbiome Impact of complementary feeding on infant gut microbiome, metabolites and early development – Yudong Shi et al – Food & Function Can longer lifespan be associated with gut microbiota involvement in lipid metabolism? – Sára Šardzíková et al – FEMS Microbiology Ecology Beneficial microbes & compounds [REVIEW] Preventive effect of probiotics on oral mucositis induced by anticancer therapy: a systematic review and meta-analysis of randomized controlled trials – Bo Yang et al – BMC Oral Health Animal Microbiome Bacteria from the Amycolatopsis genus associated with a toxic bird secrete protective secondary metabolites – Elena Seibel et al – Nature Communications Impact of virginiamycin on the ruminal microbiota of feedlot cattle – Bruna Parapinski Santos – Canadian Journal of Veterinary Research Microbiome of death From carrion to soil: microbial recycling of animal carcasses – Jennifer M. DeBruyn et al – Cell Trends in Microbiology Water & extremophile microbiome Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient – Viviana Freire-Zapata et al – Nature Microbiology Prescribed fire regimes influence responses of fungal and bacterial communities on new litter substrates in a brackish tidal marsh – Viet Q. Dao et al – PLOS One Plant, root & soil microbiome The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota – Anderson O. Oaikhena et al – Scientific Reports Water‒soil-air‒plant mutual feedback mechanism under the application of red bed composite polymers – Tianpeng Chen et al – PLOS One Diversity and community distribution of soil bacterial in the Yellow River irrigation area of Ningxia, China – Xia Wu et al – PLOS One Bioinformatics & tools Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs – Annika Jochheim et al – BMC Microbiome Posted in Animal microbiome, Built Environment Microbiology, Extremophiles, Food Microbiology, Fungi, General Microbiome, Human gut, Human oral, Metagenomics & Bioinformatics, Microbial Ecology, Microbiome of Death, Plant Root Soil microbiome, Resistome, Techniques, Water microbiome | Tagged Animal microbiome, bioinformatics, environmental microbiome, gut microbiome, gut-health, health, human microbiome, infant microbiome, microbiome, Microbiome Digest, phage, Plant microbiome, probiotics, soil, viruses | Leave a comment September 29, 2024 Posted on September 28, 2024 by JP Cardenas Human and General Microbiome Gut microbiota drives colon cancer risk associated with diet: a comparative analysis of meat-based and pesco-vegetarian diets – Carlotta De Filippo – Microbiome Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics – Georges P Schmartz – Nature Communications Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness – Minghui Cheng – Nature Communications Small Bowel Microbiome Profiles in Overweight and Obese Humans – Liqi Li – The American Journal of Gastroenterology Intratumoral microbiota as a novel prognostic indicator in bladder cancer – Yuwei Zhang – Scientific Reports Research Highlight: Identifying antimicrobials in the human microbiome – Sarah Crunkhorn – Nature Reviews. Drug Discovery Review: Akkermansia muciniphila as a Potential Guardian against Oral Health Diseases: A Narrative Review – Molly H Anderson – Nutrients Review: Intratumoral microbiota in colorectal cancer: focus on specific distribution and potential mechanisms – Jing Long – Cell Communication and Signaling Review: Bacterial extracellular vesicles at the interface of gut microbiota and immunity – Inês Melo-Marques – Gut Microbes Beneficial Microbes and Compounds GV-971 prevents severe acute pancreatitis by remodeling the microbiota-metabolic-immune axis – Xi Chen – Nature Communications Fecal Microbiota Transplantation-Mediated Rebalancing of the Gut-Brain Axis Alleviates Cisplatin-Induced Neuropathic Pain – Mousmi Rani – ACS Chemical Neuroscience FMT rescues mice from DSS-induced colitis in a STING-dependent manner – Dan Pu – Gut Microbes Aged garlic oligosaccharides modulate host metabolism and gut microbiota to alleviate high-fat and high-cholesterol diet-induced atherosclerosis in ApoE(-/-) mice – Xiaomin Wang – Food Chemistry Phytoactives for Obesity Management: Integrating Nanomedicine for Its Effective Delivery – Ashok Kumar Mandal – Nutrition Reviews Animal Microbiome Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes – Georges P Schmartz – Nature Communications Fur microbiome as a putative source of symbiotic bacteria in sucking lice – Jana Martin Říhová – Scientific Reports Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice – Feiling Huang – BMC Microbiology Dietary fiber intake impacts gut bacterial and viral populations in a hypertensive mouse model – Laura Avellaneda-Franco – Gut Microbes Effect of shipping on the microbiome of donor mice used to reconstitute germ-free recipients – Zachary L McAdams – Gut Microbes Reports Bacterial microbiome diversity along poultry slaughtering lines: insights from chicken carcasses and environmental sources – Arife Ezgi Telli – Journal of Veterinary Research The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus – Gregorio Fernandez de Landa – Microbial Ecology Gill-associated ammonia oxidizers are widespread in teleost fish – Wouter Mes – Microbiology Spectrum Microbiome Analysis: Methods, Tools and Resources Automated annotation of scientific texts for ML-based keyphrase extraction and validation – Oluwamayowa O Amusat – Database SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota – Johanna B Holm – BMC Bioinformatics Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction – Veronika Andriienko – PeerJ A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples – Krystal Thomas-White – Diagnostics Microbe-drug association prediction model based on graph convolution and attention networks – Bo Wang – Scientific Reports Posted in General Microbiome, Human gut | Tagged Animal microbiome, animal models, bioinformatics, gut microbiome, gut-health, health, human microbiome, microbiome, microbiome analysis, Microbiome Digest, probiotics | Leave a comment September 26, 2024 Posted on September 25, 2024 by Axel Künstner General microbiome [RESOURCE/COLLECTION]Microbial Primers Phages reconstitute NAD+ to counter bacterial immunity – Osterman et al. – Nature The direct inhibitory effects of Lactobacillus acidophilus, a commensal urinary bacterium, on calcium oxalate stone development – Noonin et al. – Microbiome Pregnancy and early life Neonatal gut microbiota profile and the association with retinopathy of prematurity in preterm infants – Chang et al. – Clinical & Experimental Ophthalmology Human skin microbiome The wound microbiota: microbial mechanisms of impaired wound healing and infection – Uberoi, McCready-Vangi, Grice – Nature Reviews Microbiology Human oral microbiome [PREPRINT]Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition – Zelasko et al. – bioRxiv Human gut microbiome Emergence of community behaviors in the gut microbiota upon drug treatment – Garcia-Santamarina et al. – Cell Microbial transformation of dietary xenobiotics shapes gut microbiome composition – Culp et al. – Cell [REVIEW]Microglia and Gut Microbiota: A Double-Edged Sword in Alzheimer’s Disease – Bano et al. – Ageing Research Reviews [REVIEW]What defines a healthy gut microbiome? – van Hul et al. – Gut [OUTLOOK]The gut microbiome and chronic pain – Watson – Nature Acarbose enhances the efficacy of immunotherapy against solid tumours by modulating the gut microbiota – Zhang et al. – Nature Metabolism Animal microbiome (for animals in the wild) Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores – Li et al. – Microbiome Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt) Microbial community storm dynamics signal sources of “old” stream water – URycki et al. – PLOS One Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments – Lezcano et al. – Microbiome Food microbiology Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history – Liu et al. – Cell Bioinformatics A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies – Wirbel et al. – Genome Biology [PREPRINT]Quantifying Data Distortion in Bar Graphs in Biological Research – Lin & Landry – bioRxiv Posted in Animal microbiome, Food Microbiology, General Microbiome, Human gut, Human oral, Human skin, Metabolomics, Metagenomics & Bioinformatics, Phages and viruses, Water microbiome | Tagged gut microbiome, gut-health, health, microbiome, probiotics | Leave a comment September 22, 2024 Posted on September 21, 2024 by JP Cardenas Human and General Microbiome Multi-way modelling of oral microbial dynamics and host-microbiome interactions during induced gingivitis – G R van der Ploeg – NPJ Biofilms and Microbiomes Establishing human microbial observatory programs in low- and middle-income countries – Jeffrey I Gordon – Annals of the New York Academy of Sciences Vaginal microbiota stability over 18 months in young student women in France – Jeanne Tamarelle – European Journal of Clinical Microbiology & Infectious Diseases Transfer and persistence of microbiota markers from the human hand to the knife: A preliminary study – Sukriye Karadayı – Journal of Forensic and Legal Medicine Dental Caries: The Way Forward – D T Kopycka-Kedzierawski – JDR Clinical and Translational Research Changes in the Firmicutes to Bacteriodetes ratio in the gut microbiome in individuals with anorexia nervosa following inpatient treatment: A systematic review and a case series – Passent Helal – Brain and Behavior Fusobacterium nucleatum facilitates anti-PD-1 therapy in microsatellite stable colorectal cancer – Xueliang Wang – Cancer Cell Bacterial Extracellular Vesicles as Potential Promoting Factors for Oral Lichen Planus Pathogenesis – Yu Gyung Kim – Inflammation Gut microbiota metabolite trimethylamine N-oxide promoted NAFLD progression by exacerbating intestinal barrier disruption and intrahepatic cellular imbalance – Fulin Nian – International Immunopharmacology Comment: Strengthening the foundation of African microbiome research: strategies for standardized data collection – Soumaya Kouidhi – Nature Reviews: Gastroenterology & Hepatology Review: Microbiota-gut-brain axis in health and neurological disease: Interactions between gut microbiota and the nervous system – Yuhong He – Journal of Cellular and Molecular Medicine Review: Effect of Staphylococcus aureus colonization and immune defects on the pathogenesis of atopic dermatitis – Evrim Özdemіr – Archives of Microbiology Beneficial Microbes and Compounds Gastrointestinal Self-Adaptive and Nutrient Self-Sufficient Akkermansia muciniphila-Gelatin Porous Microgels for Synergistic Therapy of Ulcerative Colitis – Yujie Zhang – ACS Nano 2′-Fucosyllactose attenuates aging-related metabolic disorders through modulating gut microbiome-T cell axis – Ang Li – Aging Cell Review: Akkermansia in the gastrointestinal tract as a modifier of human health – Maria E Panzetta – Gut Microbes Animal Microbiome (including Animal Models) Dipeptide metabolite, glutamyl-glutamate mediates microbe-host interaction to boost spermatogenesis – Balázs Juhász – Scientific Reports Intestinal deguelin drives resistance to acetaminophen-induced hepatotoxicity in female mice – Shenhai Gong – Gut Microbes Metformin reprograms tryptophan metabolism via gut Microbiome-Derived bile acid metabolites to ameliorate Depression-Like behaviors in mice – Xiaoxian Xie – Brain, Behavior, and Immunity Food Microbiome Dynamics of the microbiome and volatile organic compounds during fermentation and aging of soy sauce – Yuichi Mizuno – Journal of Bioscience and Bioengineering Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties – Matheus H Silva – BMC Genomics Plant Microbiome Pseudomonas fluorescens Inoculation Enhances Salix matsudana Growth by Modifying Phyllosphere Microbiomes, Surpassing Nitrogen Fertilization – Qing Li – Plant, cell & Environment Environmental Microbiome Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants – Zi-Yan Wei – Environmental Research Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques – Nu Ri Myeong – Scientific Data Posted in General Microbiome, Human gut | Tagged Animal microbiome, animal models, bioinformatics, environmental microbiome, human microbiome, microbiome, Microbiome Digest, Plant microbiome | Leave a comment September 19, 2024 Posted on September 18, 2024 by Axel Künstner Pregnancy and early life Networks of human milk microbiota are associated with host genomics, childhood asthma, and allergic sensitization – Fang et al. – Cell Host & Microbe Affective symptoms in pregnancy are associated with the vaginal microbiome – Scheible et al. – Journal of Affective Disorders Human oral microbiome [PREPRINT]An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research – Standeven et al. – bioRxiv Human gut microbiome [EDITORIAL]The global epidemic of early-onset cancer: Nature, nurture, or both? – Ogino & Ugai – Annals of Oncology Akkermania muciniphila: a rising star in tumor immunology – Wang & Tang – Clinical and Translational Oncology [REVIEW]Nutraceuticals and pharmacological to balance the transitional microbiome to extend immunity during COVID-19 and other viral infections – Kaushal – Animal experiments (mouse/rat experiments, chickens/pigs on different diets) The role of intestinal microbiota in physiologic and body compositional changes that accompany CLA-mediated weight loss in obese mice – Zhang et al. – Molecular Metabolism Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice – Masson et al. – Brain, Behaviour, and Immunity Succession of rumen microbiota and metabolites across different reproductive periods in different sheep breeds and their impact on the growth and development of offspring lambs – Sha et al. – Microbiome Animal microbiome (for animals in the wild) [PREPRINT]Microbiome and climate: Skin microbial diversity and community functions of Polypedates megacephalus (Anura: Rhacophoridae) associated with bioclimate – Meegaskumbura et al. – bioRxiv Plant, root, and soil microbiome Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles – Wang et al. – Microbiome Food microbiology Making yogurt with the ant holobiont uncovers bacteria, acids, and enzymes for food fermentation – Sinotte et al. – bioRxiv Phages and viruses Birth of protein folds and functions in the virome – Nomburg et al. – Nature Bioinformatics [PREPRINT]An efficient pipeline for creating metagenomic-assembled genomes from ancient oral microbiomes – Standeven et al. – bioRxiv Posted in Animal experiments, Animal microbiome, Human gut, Human oral, Human reproductive or urinary, Metagenomics & Bioinformatics, Phages and viruses, Plant Root Soil microbiome, Pregnancy and birth | Leave a comment Septiembre 15, 2024 Posted on September 15, 2024 by JP Cardenas Human and General Microbiome Correlation of gut microbial diversity to sight-threatening diabetic retinopathy – Rehana Khan – BMC Microbiology Multiomics reveals microbial metabolites as key actors in intestinal fibrosis in Crohn’s disease – Xuehua Li – EMBO Molecular Medicine Inflammation mediated by gut microbiome alterations promotes lung cancer development and an immunosuppressed tumor microenvironment – Zahraa Rahal – Cancer Immunology Research Microbial interactions impact stress tolerance in a model oral community – Gina R Lewin – Microbiology Spectrum The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen – Min Bai – Journal of Ethnopharmacology Enteric-coated cerium dioxide nanoparticles for effective inflammatory bowel disease treatment by regulating the redox balance and gut microbiome – Yubiao Huang – Biomaterials Review: Micro- and nano-plastics, intestinal inflammation, and inflammatory bowel disease: A review of the literature – Manasi Agrawal – The Science of the Total Environment Commentary:  The 3 Ds: Depression, Dysbiosis, and Clostridiodes difficile – Antoine Boustany – Advances in Therapy Research Highlight: Targeting fatty acid metabolism promotes a healthy vaginal microbiome – Iris Marchal – Nature Biotechnology Animal Microbiome Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan – Kosuke Takada – FEBS Open Bio From Skin to Gut: Understanding Microbial Diversity in Rana amurensis and R. dybowskii – Ming-He Yang – Current Microbiology Plant and Soil Microbiome Ridge planting increases the rhizosphere microbiome diversity and improves the yield of Pinellia ternata (Thunb.) Breit in North China – Yaofa Li – PloS One Microbiome Analysis Forum: Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities – Nicholas A Bokulich – Trends in Microbiology Posted in General Microbiome, Human gut | Tagged Animal microbiome, animal models, bioinformatics, environmental microbiome, microbiome, Microbiome Digest, Plant microbiome | Leave a comment September 13, 2024 Posted on September 13, 2024 by Svetlana Ugarcina Perovic Happy Friday! And, see you next week at the MVIF and African Microbiome Day events! Big news for #microbiome researchers:The new #MVIF talk format is a game-changer! .@lisakarstens and I just discussed how 🎆MicroTalks🎆 are awesome, let us break down for you WHY…1/5 https://t.co/cVwOXaNqRC— Svetlana U. Perović (@svetlana_up) September 10, 2024 Human microbiome Gut Microbiome Transient colonizing microbes promote gut dysbiosis and functional impairment – Sunjae Lee – npj Biofilms and Microbiomes Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome – Laura Wosinska – Microbiome Research Reports Gut microbiome and schizophrenia: insights from two-sample Mendelian randomization – Keer Zhou – Schizophrenia Disease-associated microbiome signature species in the gut – Junhui Li – PNAS Nexus Nasal microbiome E-Cigarette Use, Cigarette Smoking, and Sex Are Associated With Nasal Microbiome Dysbiosis Get access Arrow – Elise Hickman – Nicotine & Tobacco Research Urinary microbiome Review: Synthesis of current pediatric urinary microbiome research – Layla M. Jeries – Frontiers in Pediatrics Highlights of our recent study with @lisakarstens and @DnpKelly on pediatric urobiome: https://t.co/fziYMu2tsYHappy to be part of the team and continue parsing this novel microbial niche's development and functioning!— @microrocket@mastodon.social (@MicroRocket) September 7, 2024 Skin microbiome The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival – Philipp Licht – npj Biofilms and Microbiomes Animal microbiome Antibiotics damage the colonic mucus barrier in a microbiota-independent manner – Jasmin Sawaed – Science Advances 🚨🚨I’m excited to present our lab’s new paper where we tried to provide a mechanistic explanation for the link between antibiotic use and risk of developing inflammatory bowel diseases (#IBD). A 🧵/1https://t.co/k2wUPoIwTm— Shai Bel (@Mucus_Man) September 11, 2024 Host diet drives gut microbiome convergence between coral reef fishes and mammals – Samuel Degregori – Molecular Ecology Functional insights into the effect of feralisation on the gut microbiota of cats worldwide – Ostaizka Aizpurua – bioRxiv Feral 😼 and domestic 😺 cats don’t just differ in behaviour; their gut microbiomes are also distinct. These differences could even play a role in shaping their unique behaviours… 🤔. Congrats for the wonderful effort, team!https://t.co/M6E3SlU82Z pic.twitter.com/49m9VL0dA6— Antton Alberdi (@anttonio) September 11, 2024 Animal experiments Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury – Adam M. Hamilton – npj Biofilms and Microbiomes Ketogenic interventions restore cognition and modulate peripheral metabolic dysfunctions in Alzheimer’s disease mouse models – Paule E. H. M’Bra – bioRxiv Plant microbiome The influence of plant traits on soil microbial communities varies between arid and mesic grasslands – Eleonora Egidi – Plant and Soil New paper out 🚨 The influence of plant traits on soil microbial communities varies between arid and mesic grasslandsPublished today in @plantandsoil Read at:https://t.co/WnUMJSjVxC— Eleonora Egidi (she/her) (@EleonoraEgidi) August 14, 2024 Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles – Haitao Wang – Microbiome Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes – F. Fracchia – Microbiome Built environment Predicting how varying moisture conditions impact the microbiome of dust collected from the International Space Station – Nicholas Nastasi – Microbiom The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches – Kenneth Wasmund – Environmental Microbiology How do microbes in #WWTPs break down complex organics? Our latest study lead by @KennethWasmund into dives the secreted proteomes of over 1,000 #MAGs from Danish WWTPs. Revealing new insights into the key microbial functions in nutrient cycling!https://t.co/gVdKMwJqyR— Morten Kam Dahl Dueholm (@msdueholm) September 12, 2024 Bioinformatics Microbial network inference for longitudinal microbiome studies with LUPINE – Saritha Kodikara, Kim-Anh Le Cao – bioRxiv This is such an #important #microbiome webinar – please share this invitation to the third annual #africanmicrobiomeday@H3ABioNet pic.twitter.com/QVa2SA4MsG— Jo-Ann Passmore (@MucosalGroup) June 28, 2024 Posted in Animal experiments, Animal microbiome, Built Environment Microbiology, Events and jobs, General Microbiome, Human gut, Human oral, Human reproductive or urinary, Human skin, Metagenomics & Bioinformatics, Microbial Ecology, Plant Root Soil microbiome, Resistome, Water microbiome | Leave a comment September 12, 2024 Posted on September 11, 2024 by Axel Künstner General microbiome [REVIEW]Emerging roles of intratumor microbiota in cancer: tumorigenesis and management strategies – Shi, Li & Zhang – Journal of Translational Medicine [REVIEW]Fungal effectors: past, present, and future – Li et al. – Current Opinion in Microbiology [Voices]Microbes and metabolites in immunity – Elinav et al. – Immunity Pregnancy and early life Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome – Johnson et al. – Cell Genomics Human urinary tract microbiome [REVIEW]Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics – Timm, Russell & Hultgren Human gut microbiome Dietary-timing-induced gut microbiota diurnal oscillations modulate inflammatory rhythms in rheumatoid arthritis – Ma et al. – Cell Metabolism Animal microbiome [PREPRINT]The holobiont’s extracellular microbiome modulates the adaptation of an intracellular endosymbiont – Imchen et al. – bioRxiv [PREPRINT]Functional insights into the effect of feralisation on the gut microbiota of cats worldwide – Aizpurua et al. – bioRxiv Microbial community profiling in intestinal tract of indigenous chickens from different villages – Mootane et al. – Scientific Reports Vitamin B12 ameliorates gut epithelial injury via modulating the HIF-1 pathway and gut microbiota – Feng et al. – Cellular and Molecular Life Sciences [PREPRINT]Symbiont loss and gain, rather than co-diversification shapes honeybee gut microbiota diversity and function – Prasad et al. – bioRxiv [PREPRINT]Effects of parental care on skin microbial community composition in poison frogs – Fischer et al. – bioRxiv Plant, root, and soil microbiome Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot – Wang et al. – Microbiome [REVIEW]Re-Envisioning the Plant Disease Triangle: Full Integration of the Host Microbiota and a Focal Pivot to Health Outcomes – Leveau – Annual Review of Phytopathology Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt) Global marine microbial diversity and its potential in bioprospecting – Chen et al. – Nature Bioinformatics Stable biomarker discovery in multi-omics data via canonical correlation analysis – Pusa & Rousu – PLOS One Techniques Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples – Li et al. – Microbiome Posted in Animal experiments, Animal microbiome, Fungi, General Microbiome, Human gut, Human reproductive or urinary, Metagenomics & Bioinformatics, Microbial Ecology, Plant Root Soil microbiome, Pregnancy and birth, Techniques, Water microbiome | Leave a comment Post navigation ← Older posts Search Recent Posts October 6, 2024 October 4, 2024 October 2, 2024 September 29, 2024 September 26, 2024 September 22, 2024 September 19, 2024 Septiembre 15, 2024 September 13, 2024 September 12, 2024 Recent Comments Best Practice Exchan… on June 1, 2018May 17, 2024 | Micro… on May 15, 2024Kathy Brown on The Hetch Hetchy RailroadJohn Wilbur on The Hetch Hetchy RailroadHavana Nguyen on December 16, 2019 Archives Archives Select Month October 2024 September 2024 August 2024 July 2024 June 2024 May 2024 April 2024 March 2024 February 2024 January 2024 December 2023 November 2023 October 2023 September 2023 August 2023 July 2023 June 2023 May 2023 April 2023 March 2023 February 2023 January 2023 December 2022 November 2022 October 2022 September 2022 August 2022 July 2022 June 2022 May 2022 April 2022 March 2022 February 2022 January 2022 December 2021 November 2021 October 2021 September 2021 August 2021 July 2021 June 2021 May 2021 April 2021 March 2021 February 2021 January 2021 December 2020 November 2020 October 2020 September 2020 August 2020 July 2020 June 2020 May 2020 April 2020 March 2020 February 2020 January 2020 December 2019 November 2019 October 2019 September 2019 August 2019 July 2019 June 2019 May 2019 April 2019 March 2019 February 2019 January 2019 December 2018 November 2018 October 2018 September 2018 August 2018 July 2018 June 2018 May 2018 April 2018 March 2018 February 2018 January 2018 December 2017 November 2017 October 2017 September 2017 August 2017 July 2017 June 2017 May 2017 April 2017 March 2017 February 2017 January 2017 December 2016 November 2016 October 2016 September 2016 August 2016 July 2016 June 2016 May 2016 April 2016 March 2016 February 2016 January 2016 December 2015 November 2015 October 2015 September 2015 August 2015 July 2015 June 2015 May 2015 April 2015 March 2015 February 2015 January 2015 December 2014 November 2014 October 2014 September 2014 August 2014 July 2014 June 2014 May 2014 CategoriesCategories Select Category About this blog Air microbiome Animal experiments Animal microbiome Archaea Bacteria Hysteria Bik’s Non-Microbiology Picks Built Environment Microbiology Events and jobs Extremophiles Fecal Transplants Food Microbiology Fun Functional foods Fungi General Microbiome Human gut Human oral Human reproductive or urinary Human respiratory Human skin Infection and transplantation Journal club Metabolomics Metagenomics & Bioinformatics Microbes and the market Microbes in the News Microbial Ecology Microbiome of Death More Microbes Near-sterile sites Peer Review Phages and viruses Plant Root Soil microbiome Pregnancy and birth Pseudoscience and quackery Resistome Science – Career – Publishing Science and Art Science Integrity Techniques Transcriptomics Proteomics Uncategorized Waste and pollution Water microbiome Follow me on TwitterMy TweetsBlogroll Aetiology Bits of DNA For Better Science Microbe Post MicrobeBlog MicroBEnet Blog Microbes Rule MO BIO Microbiome News Mostly Microbes Small Things Considered the MACROSCOPE The Microbial Menagerie The Tree of Life ViroBlogy Blog at WordPress.com. 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