Category Archives: General Microbiome

October 13, 2024

Posted on by

Human and General Microbiome

Aggregatibacter is inversely associated with inflammatory mediators in sputa of patients with chronic airway diseases and reduces inflammation in vitro – Ellen Goeteyn – Respiratory Research

Oral Microbiota Development in the First 60 Months: A Longitudinal Study – K Yama – Journal of Dental Research

Microbiome-derived metabolites in early to mid-pregnancy and risk of gestational diabetes: a metabolome-wide association study – Sita Manasa Susarla – BMC Medicine

Unique Gut Microbiome and Metabolic Profiles in Chinese Workers Exposed to Dust: Insights from a Case-Control Study – Xiaojun Qian – Journal of Occupational and Environmental Medicine

Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population – Hyun Sik Kim – Scientific Reports

A search for bacteria identified from cerebrospinal fluid shunt infections in previous surgical events – Paul Hodor – PloS One

Microbiome and metabolome patterns after lung transplantation reflect underlying disease and chronic lung allograft dysfunction – Christian Martin – Microbiome

Review: Reexamining the role of Fusobacterium nucleatum subspecies in clinical and experimental studies – Madeline Krieger – Gut Microbes

Review: Host-microbe interaction paradigms in acute and recurrent vulvovaginal candidiasis – Jessie MacAlpine – Cell Host & Microbe

Review: Balancing act: counteracting adverse drug effects on the microbiome – Jacobo de la Cuesta-Zuluaga – Trends in Microbiology

Cancer Research

Preview: Gut microbiome and bladder cancer: A new link through nitrosamine metabolism – Sridhar Mani – Cell Host & Microbe

Review: Prostate cancer microenvironment: multidimensional regulation of immune cells, vascular system, stromal cells, and microbiota – Lin Chen – Molecular Cancer

Review: Gut and oral microbiota in gynecological cancers: interaction, mechanism, and therapeutic value – Jian Wu – NPJ Biofilms and Microbiomes

Beneficial Microbes and Compounds

Effects of complex probiotics on intestinal function and its regulatory mechanism in patients with constipation – X Zhang – Beneficial Microbes

Lactiplantibacillus plantarum P101 Alleviated Alcohol-Induced Hepatic Lipid Accumulation in Mice via AMPK Signaling Pathway: Gut Microbiota and Metabolomics Analysis – Xiaoyan Feng – Probiotics and Antimicrobial Proteins

Preview: Unlocking the genetic influence on milk variation and its potential implication for infant health – Claudia Nussbaum – Cell Genomics

Review: The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer – Nathalie M Delzenne – Nature Reviews. Microbiology

Review: Microbiome-based therapeutics for Parkinson’s disease – Adam M Hamilton – Neurotherapeutics

Animal Microbiome

Gut bacteria of lepidopteran herbivores facilitate digestion of plant toxins – Nan Zhang – PNAS

Sea cucumbers and their symbiotic microbiome have evolved to feed on seabed sediments – Wenjie Pan – Nature Communications

Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods – Tobyn Branck – The ISME Journal

Review: Quantitative Synthesis of Microbe-Driven Acclimation and Adaptation in Wild Vertebrates – Garazi Martin Bideguren – Evolutionary Applications

Plant Microbiome

The role of foraging pollinators in assembling the flower microbiota and transmitting the fire blight pathogen Erwinia amylovora – Salma Mukhtar – Environmental Microbiology

Environmental Microbiome

Distinct microbial communities supported by iron oxidation – Kateřina Burkartová – Environmental Microbiology

Microbiome Analysis: Tools, Techniques and Resources

Normalization of short-chain fatty acid concentration by bacterial count of stool samples improves discrimination between eubiotic and dysbiotic gut microbiota caused by Clostridioides difficile infection – Anna Sayol-Altarriba – Gut Microbes

SmT/SHM-seq: simultaneously capturing spatial transcriptome and microbiome information in plants – Peng Mu – Trends in Plant Science

High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform – Xuan Lin – PNAS Nexus

A deployable film method to enable replicable sampling of low-abundance environmental microbiomes – Phoebe Mankiewicz Ledins – Scientific Reports

October 6, 2024

Posted on by

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

October 4, 2024

Posted on by

Happy Friday! And see you next week at MVIF!

Plastisphere microbiome

What harmful microbes are lurking in the world’s 7 billion tonnes of plastic waste? – Changchao Li – Nature

Respiratory 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

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

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

Photoperiod effects on corticosterone and seasonal clocks in cafeteria-induced obese fischer 344 rats are influenced by gut microbiota – Verónica Arreaza-Gil – Scientific Reports 

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 microbiome

Making 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

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

October 2, 2024

Posted on by

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

September 29, 2024

Posted on by

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

September 26, 2024

Posted on by

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

September 22, 2024

Posted on by

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

Septiembre 15, 2024

Posted on by

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

September 13, 2024

Posted on by

Happy Friday!
And, see you next week at the MVIF and African Microbiome Day events!

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

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

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

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

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

Bioinformatics

Microbial network inference for longitudinal microbiome studies with LUPINE – Saritha Kodikara, Kim-Anh Le Cao – bioRxiv

September 12, 2024

Posted on by

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