Tag Archives: environmental microbiome

July 31, 2024

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Human gut microbiome

The gut mycobiome signatures in long-lived populations – Lixia Pu et al – Cell iScience

Viral metagenomics combined with non-targeted serum metabolomics reveals the role of enteroviruses in a mouse model of coronary heart disease – Xiang Li et al – BMC Virology

Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria – Ting Zhang et al – ISME Journal

Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota – David Bars-Cortina et al – BMC Genomics

Effect of different delivery modes on intestinal microbiota and immune function of neonates – Chunhui Lai et al – Scientific Reports

Animal experiments

Effects of Akkermansia muciniphila on Gut Morphology, Antioxidant Indices, and Gut Microbiome of Mice Under Heat Stress – Caiyu Luo et al – Foodborne Pathogens and Disease

Gut microbiota mediates the anti-inflammatory effects of supplemental infrared irradiation in mice – Shijing Wang et al – Photochemistry and Photobiology

Short-chain fatty acids ameliorate imiquimod-induced skin thickening and IL-17 levels and alter gut microbiota in mice: a metagenomic association analysis – Yi-Ju Chen et al – Scientific Reports

Animal microbiome

Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus – Masayuki Kaneko et al – ISME Communications

Rodents consuming the same toxic diet harbor a unique functional core microbiome – Tess E. Stapleton et al – BMC Animal Microbiome

The plant-sucking insect selects assembly of the gut microbiota from environment to enhance host reproduction – Hong-Wei Shan et al – NPJ Biofilms and Microbiomes

Alterations in captive Alexandrine parakeet (Palaeornis eupatria) gut microbiome and metabolome in response to dietary change – Xin Feng et al – Comparative Biochemistry and Physiology

Link between bacterial communities and contrasted loads in ectoparasitic monogeneans from the external mucus of two wild sparid species (Teleostei) – Judith Revault et al – BMC Animal Microbiome

Beneficial microbes and compounds

Unearthing Lactococcus lactis and Scheffersomyeces symbionts from edible wood-boring beetle larvae as a bio-resource for industrial applications – Shadrick Kibet et al – BMC Microbiology

Plant, root, and soil microbiome

[OPINION] Microbiome Bioprospecting for Sustainable Agrobiome and Circular Bioeconomy – Dhananjaya Pratap Singh – Anthropocene Science

Host genetic variation and specialized metabolites from wheat leaves enriches for phyllosphere Pseudomonas spp. with enriched antibiotic resistomes – Qian Xiang et al – ISME Journal

Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health – Morgane Duret et al – Microbiological Research

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan – Kohei Hamamoto et al – BMC Environmental Microbiome

July 28, 2024

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Human and General Microbiome

Shaping Microbiota During the First 1000 Days of Life – Anna Samarra – Advances in Experimental Medicine and Biology

Role of sulfidogenic members of the gut microbiota in human disease – Andreia I Pimenta – Advances in Microbial Physiology

Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor – Yunjae Kim – Cell Host & Microbe

Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort – Taona Emmah Mudhluli – BMC Genomics

Gut microbial features and circulating metabolomic signatures of frailty in older adults – Yanni Pu – Nature Aging

Gut microbiome and metabolome signatures in liver cirrhosis-related complications – Satya Priya Sharma – Clinical and Molecular Hepatology

Detection of Microplastics in Human Breast Milk and Its Association with Changes in Human Milk Bacterial Microbiota – Apisith Saraluck – Journal of Clinical Medicine

Regional Differences in Microbial Infiltration of Brain Tissue from Alzheimer’s Disease Patients and Control Individuals – T Bucky Jones – Brain Sciences

Review: Aggregatibacter actinomycetemcomitans: From the Oral Cavity to the Heart Valves – Jasminka Talapko – Microorganisms

Beneficial Microbes and Compounds

Review: Digesting the complex metabolic effects of diet on the host and microbiome – Rachel N Carmody – Cell

Review: A comprehensive review of synbiotics: an emerging paradigm in health promotion and disease management – Sulhee Lee – World Journal of Microbiology & Biotechnology

Animal Model Microbiome

Desulfovibrio vulgaris caused gut inflammation and aggravated DSS-induced colitis in C57BL/6 mice model – Guoxin Huang – Gut Pathogens

LCN2 regulates the gut microbiota and metabolic profile in mice infected with Mycobacterium bovis – Quntao Huang – mSystems

Non-Model Animal Microbiome

Multiomics of parkinsonism cynomolgus monkeys highlights significance of metabolites in interaction between host and microbiota – Jiang-Mei Gao – NPJ Biofilms and Microbiomes

Vaginal and Uterine Microbiota of Healthy Maiden Mares during Estrus – Ana Gil-Miranda – Veterinary Sciences

Review: Reproductive Tract Microbiota of Mares – Ana Gil-Miranda – Veterinary Sciences

Environmental Microbiology

Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances – Mafalda S Baptista – Environmental Microbiome

Plant Microbiome

Thermal sensitivity of soil microbial carbon use efficiency across forest biomes – Chengjie Ren – Nature Communications

Miscanthus sp. root exudate alters rhizosphere microbial community to drive soil aggregation for heavy metal immobilization – Bohan Wu – The Science of the Total Environment

Soil conditions modify species diversity effects on tree functional trait expression – Andréa Davrinche – Scientific Reports

Microbiome Analysis

A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction – Tatiana Y Fofanova – PloS ONE

Compositional Data and Microbiota Analysis: Imagination and Reality – Tatsuki Itagaki – Microorganisms

Thanos: An R Package for the Gene-Centric Analysis of Functional Potential in Metagenomic Samples – Zhe Zhao – Microorganisms

July 24, 2024

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Human microbiome

Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease – Xiangge Tian et al – BMC Microbiome

The Role of Gut Microbiota in the Neuroprotective Effects of Selenium in Alzheimer’s Disease – Anatoly V. Skalny et al – Molecular Neurobiology

[REVIEW] The oral–gut microbiome axis in health and disease – Benoit J. Kunath – Nature Reviews Microbiology

Enhancing gut microbiota and microbial function with inulin supplementation in children with obesity – Chonnikant Visuthranukul et al – International Journal of Obesity

Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder – Zaiquan Dong et al – Journal of Affective Disorders

Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health – Na Han et al – Frontiers in Microbiology

Skin locations inference and body fluid identification from skin microbial patterns for forensic applications – Litao Huang et al – Forensic Science International

Animal experiments

Improving insulin resistance by sulforaphane via activating the Bacteroides and Lactobacillus SCFAs–GPR–GLP1 signal axis – Sicong Tian et al – Food & Function

Gastroprotective and microbiome-modulating effects of ubiquinol in rats with radiation-induced enteropathy – Walaa A. Eraqi et al – BMC Animal Microbiome

Animal microbiome

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses – Mason R. Stothart et al – Nature Communications

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale – Shuai Du et al – Environmental Science & Technology

Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages – Marwa Mamdouh Tawfik et al – BMC Animal Microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Laura Glendinning et al – BMC Microbiome

Water & extremophile microbiome

Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton – Tianyi Chang et al – BMC Microbiome

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake – Arianna I. Krinos et al – BMC Microbiome

Built environment microbiome

[PREPRINT] Utilizing the biosimulator to analyze the environmental microbiome within the intensive care units of a hospital – Sunil Thomas et al – ResearchSquare

Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system – Dou Wang et al – BMC Microbiome

Plant, root, & soil microbiome

Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China – Jie-Liang Liang et al – BMC Microbiome

Bioinformatics tools

MIDASim: a fast and simple simulator for realistic microbiome data – Mengyu He et al – BMC Microbiome

July 21, 2024

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Human and General Microbiome

Akkermansia muciniphila and Parabacteroides distasonis as prognostic markers for relapse in ulcerative colitis patients – Ana Mendes-Frias – Frontiers in Cellular and Infection Microbiology

Obesity-enriched gut microbe degrades myo-inositol and promotes lipid absorption – Chao Wu – Cell Host & Microbe

Gut microbiome in endometriosis: a cohort study on 1000 individuals – Inmaculada Pérez-Prieto – BMC Medicine

Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer – Pan Zhang – Journal of Medical Virology

The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors – Caroline E Dravillas – Cancer Research Communications

Gut microbiome diversity within Clostridia is negatively associated with human obesity – Laura Salazar-Jaramillo – mSystems

Early depletion of gut microbiota shape oligodendrocyte response after traumatic brain injury – Kirill Shumilov – Journal of Neuroinflammation

Effect of progestin-based contraceptives on HIV-associated vaginal immune biomarkers and microbiome in adolescent girls – Mélodie A Nasr – PloS One

Review: Microbiome and pancreatic cancer: time to think about chemotherapy – Juliana de Castilhos – Gut Microbes

Review: Host control of the microbiome: Mechanisms, evolution, and disease – Jacob Wilde – Science

Review: Connecting microbial community assembly and function – Leonora S Bittleston – Current Opinion in Microbiology

Review: Microbiota of Saliva: A Non-invasive Diagnostic Tool – Dasharath B Shinde – Indian Journal of Microbiology

Beneficial Microbes, Compounds and Interventions

Topical prebiotic nitrate: optimizing the ‘hang-time’, source and dose for specific oral or systemic effects – Bob T Rosier – NPJ Biofilms and Microbiomes

An improved diet-based nutritional interventions can improve childhood obesity with the synergistic regulation of gut microbiota – M Zhou – Beneficial Microbes

Intermittent fasting, calorie restriction, and a ketogenic diet improve mitochondrial function by reducing lipopolysaccharide signaling in monocytes during obesity: A randomized clinical trial – Martha Guevara-Cruz – Clinical Nutrition 

Food Microbiome

Influence of the initial microbiota on eggplant shibazuke pickle and eggplant juice fermentation – Kazunori Sawada – Microbiology Spectrum

Metatranscriptomics reveals microbial community function succession and characteristic flavor formation mechanisms during black rice wine fermentation – Aoxing Tang – Food Chemistry

Animal Model Microbiome

Gα13 restricts nutrient driven proliferation in mucosal germinal centers – Hang T Nguyen – Nature Immunology

Gut microbiota mediates ambient PM(2.5) exposure-induced abnormal glucose metabolism via short-chain fatty acids – Wenpu Shao – Journal of Hazardous Materials

Non-Model Animal Microbiome

Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants – Christian Cabuslay – Molecular Ecology

Review: The interplay between gut symbionts and behavioral variation in social insects – Joanito Liberti – Current Opinion in Insect Science

Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease – Wei-Chen Wu – mSphere

Alcohol consumption during pregnancy differentially affects the fecal microbiota of dams and offspring – Tamara S Bodnar – Scientific Reports

Environmental Microbiome

Meta-omics analysis reveals the marine arsenic cycle driven by bacteria – Zhao-Jie Teng – Journal of Hazardous Materials

Using Machine Learning to Identify Environmental Factors that Collectively Determine Microbial Community Structure of Activated Sludge – Lu Wang – Environmental Research

Microplastic pollution promotes soil respiration: A global-scale meta-analysis – Shuling Zhao – Global Change Biology

SMMP: A Deep-Coverage Marine Metaproteome Method for Microbial Community Analysis throughout the Water Column Using 1 L of Seawater – Songduo Wang – Analytical Chemistry

Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau – Luyao Kang – Nature Communications

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass – Xuejiao Lyu – Journal of Industrial Microbiology & Biotechnology

Microbiome Analysis

GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs – Jianshu Zhao – Nucleic Acids Research

Multi-omics machine learning to study host-microbiome interactions in early-onset colorectal cancer – Thejus T Jayakrishnan – NPJ Precision Oncology

3D printed rectal swabs for assessing the gut microbiome, metabolome and inflammation – Robert W Perry – Scientific Reports

AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides – Amin Darabi – BMC Bioinformatics

JASPER: Fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression – Joelle Mbatchou – American Journal of Human Genetics

Microbial Evolution

The nature of the last universal common ancestor and its impact on the early Earth system – Edmund R R Moody – Nature Ecology & Evolution

July 7, 2024

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Human and General Microbiome

Changes in the gut microbiome of patients with esophageal cancer: a systematic review and meta-analysis based on 16S gene sequencing technology – Jieyin Deng – Microbial Pathogenesis

Integrated metagenomic and metabolomic analysis reveals distinctive stage-specific gut-microbiome-derived metabolites in intracranial aneurysms – Haitao Sun – Gut

After surgically induced remission, ileal and colonic mucosa-associated microbiota predicts Crohn’s disease recurrence – Cristian-Hernandez Rocha – Clinical Gastroenterology and Hepatology

Human gut microbiota analysis of cystic fibrosis infants using metaproteomics – C García-Durán – Microbiology Resource Announcements

Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages – Shivkumar Vishnempet Shridhar – Cell Reports

Perturbations in gut microbiota composition in schizophrenia – YiMeng Wang – PloS One

Maternal gestational diabetes mellitus associates with altered gut microbiome composition and head circumference abnormalities in male offspring – Shilan Wang – Cell host & Microbe

Microbial signatures and continuum in endometrial cancer and benign patients – Anita Semertzidou – Microbiome

Comparison of shipping versus immediate freezer storage of vaginal samples for vaginal microbiota assessment – Susan Tuddenham – Sexually Transmitted Infections

Letter: Real-world bisphenol A exposure not linked to microbiota dynamics in childhood obesity – Robyn L Prueitt – mSystems

Essay: Blockbuster T cells in the gut: A high-resolution view of immune modulation by the gut microbiome is presented – Kazuki Nagashima – Science

Review: Gut microbiota-lncRNA/circRNA crosstalk: implications for different diseases – Lei Zhang – Critical Reviews in Microbiology

Review: The role of gut microbiota, exosomes, and their interaction in the pathogenesis of ALD – Zilu Cheng – Journal of Advanced Research

Review: Integrating host and microbiome biology using holo-omics – Carl M Kobel – Molecular Omics

Beneficial Microbes, Compounds, and Interventions

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments – Torben Sølbeck Rasmussen – Microbiome

Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity – Michele Zuppi – Microbiome

A meta-analysis of randomized controlled trials evaluating the effectiveness of fecal microbiota transplantation for patients with irritable bowel syndrome – Yu Wang – BMC Gastroenterology

Faecalibaterium prausnitzii strain EXL01 boosts efficacy of immune checkpoint inhibitors – Marius Bredon – Oncoimmunology

Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer’s disease – Annalise Schweickart – NPJ Metabolic Health and Disease

Oral histidine affects gut microbiota and MAIT cells improving glycemic control in type 2 diabetes patients – Moritz V Warmbrunn – Gut Microbes

The Evolution of Science and Regulation of Dietary Supplements: Past, Present, and Future – Paul M Coates – The Journal of Nutrition

Review: Dietary patterns interfere with gut microbiota to combat obesity – Xiaofan Lou – Frontiers in Nutrition

Plant Microbiome

Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health – Sang-Moo Lee – The ISME Journal

Review: Unearthing the power of microbes as plant microbiome for sustainable agriculture – Arpan Mukherjee – Microbiological Research

Review: Surviving the Stress: Understanding the Molecular Basis of Plant Adaptations and Uncovering the Role of Mycorrhizal Association in Plant Abiotic Stresses – Vivek Sharma – Microbial Pathogenesis

Environmental Microbiome

The drainome: longitudinal metagenomic characterisation of wastewater from hospital ward sinks to characterize the microbiome and resistome and assess the effects of decontamination interventions – Luke B Snell – The Journal of Hospital Infection

Review: Beyond Meta-Omics: Functional Genomics in Future Marine Microbiome Research – Yin Chen – Annual Review of Marine Science

Review: Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges – Haixia Pan – Current Microbiology

Forensic Microbiome

16S rRNA, metagenomics and 2bRAD-M sequencing to decode human thanatomicrobiome – Xin Huang – Scientific Data

Microbiome Analysis

A graph neural network approach for predicting drug susceptibility in the human microbiome – Maryam – Computers in Biology and Medicine

Protocol for the construction and functional profiling of metagenome-assembled genomes for microbiome analyses – Goutam Banerjee – STAR Protocols

DeepPIG: deep neural network architecture with pairwise connected layers and stochastic gates using knockoff frameworks for feature selection – Euiyoung Oh – Scientific Reports

CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets – Orges Koci – Microbiome

June 30, 2024

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Human and General Microbiome

Gut

Metaproteomic portrait of the healthy human gut microbiota – Alessandro Tanca – NPJ Biofilms and Microbiomes

Microbiome and Growth in Infants with Congenital Heart Disease – Michael P Fundora – The Journal of Pediatrics

Driving gut microbiota enterotypes through host genetics – Catherine Larzul – Microbiome

Obesity-associated microbiomes instigate visceral adipose tissue inflammation by recruitment of distinct neutrophils – Dharti Shantaram – Nature Communications

Fecal, Duodenal and Tumor Microbiota Composition of Esophageal Carcinoma Patients, a Longitudinal Prospective Cohort – Tom van den Ende – Journal of the National Cancer Institute

Review: Role of the intestinal microbiota in contributing to weight disorders and associated comorbidities – Matthias Van Hul – Clinical Microbiology Reviews

Review: The role of the gut microbiome in disorders of gut-brain interaction – Brent J Gawey – The FEBS Journal

Skin

Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin – Tianze Yu – Cell Host & Microbe

Genitourinary Tract

Vaginal anaerobes are associated with cervicitis: a case-control study – Erica L Plummer – The Journal of Infection

Oral and Respiratory Tract

Review: The Impact of Oral Diseases on Respiratory Health and the Influence of Respiratory Infections on the Oral Microbiome – Annapurna Gupta – Journal of Dentistry

Beneficial Microbes and Compounds

Lactobacillus acidophilus protects against Corynebacterium pseudotuberculosis infection by regulating the autophagy of macrophages and maintaining gut microbiota homeostasis in C57BL/6 mice – Dengliang Li – mSystems

Exploring novel microbial metabolites and drugs for inhibiting Clostridioides difficile – Ahmed A Abouelkhair – mSphere

Ketogenic diet-induced bile acids protect against obesity through reduced calorie absorption – Xiao Li – Nature Metabolism

Review: How Diet and Lifestyle Can Fine-Tune Gut Microbiomes for Healthy Aging – M Tamayo – Annual Review of Food Science and Technology

Animal Microbiome

Gut microbiota signatures of vulnerability to food addiction in mice and humans – Solveiga Samulėnaitė – Gut

Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate – Peter M Finnegan – mSphere

Maternal transmission as a microbial symbiont sieve, and the absence of lactation in male mammals – Brennen T Fagan – Nature Communications

Built Environment Microbiome

A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal – Sarbanding Sané – Scientific Reports

Microbiome Analysis: Tools, Techniques and Resources

Compositionally aware estimation of cross-correlations for microbiome data – Ib Thorsgaard Jensen – PloS ONE

Bioinformatic Workflows for Metaproteomics – Tanja Holstein – Methods in Molecular Biology 

Floria: fast and accurate strain haplotyping in metagenomes – Jim Shaw – Bioinformatics 

Enhancing antimicrobial resistance detection with MetaGeneMiner: Targeted gene extraction from metagenomes – Chang Liu – Chinese Medical Journal

Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics – Alessandro Tanca – mSystems

Genome Watch: Bacterial barcoding facilitates plant microbiome studies – Hualan Liu – Nature Reviews Microbiology

Other

Retraction Note: Microbiome analyses of blood and tissues suggest cancer diagnostic approach – Gregory D Poore – Nature

June 23, 2024

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Human and General Microbiome

Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome – Lisa Derosa – Cell

News: Gut microbiome discovery provides roadmap for life-saving cancer therapies – Giorgia Guglielmi – Nature

Faecal microbiota transplantation for sleep disturbance in post-acute COVID-19 syndrome – Raphaela I Lau – Clinical Gastroenterology and Hepatology

Pan-cancer atlas of tumor-resident microbiome, immunity and prognosis – Dashuang Sheng – Cancer Letters

Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers – Anju R Nath – Genomics & Informatics

A Bioinformatic Analysis of Gut Microbiota Related with Immune Cell Infiltration in Colorectal Cancer – Dan Liu – Cancer Investigation

An alternative broad-specificity pathway for glycan breakdown in bacteria – Seyed Amirhossein Nasseri – Nature

The association of maternal factors with the neonatal microbiota and health – Bin Zhu – Nature Communications

Revealing the gut microbiome mystery: A meta-analysis revealing differences between individuals with autism spectrum disorder and neurotypical children – Changjiang Yang – Bioscience Trends

Propionic acid promotes neurite recovery in damaged multiple sclerosis neurons – Barbara Gisevius – Brain Communications

Review: What is the impact of microbiota on dry eye: a literature review of the gut-eye axis – Jiaping Song – BMC Ophthalmology

Review: Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health – Meifang Xiao – NPJ Biofilms and Microbiomes

Review: Peyer’s Patch: Possible target for modulating the Gut-Brain-Axis through microbiota – Reza Asgari – Cellular Immunology

Animal Model Microbiome

Alterations in gut microbiota and inflammatory cytokines after administration of antibiotics in mice – Wang Gao – Microbiology Spectrum

Environmental Microbiome

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts – Emily B Graham – Nature Microbiology

Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome – Emanuela Buschi – Science Advances

Microbial co-occurrence network demonstrates spatial and climatic trends for global soil diversity – Nikos Pechlivanis – Scientific Data

Other Microbes

Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries – Felipe Senne de Oliveira Lino – Nature Communications

Microbiome Analysis: tools, techniques and resources

A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome – Liansha Huang – Nature Microbiology

Deep learning for predicting 16S rRNA gene copy number – Jiazheng Miao – Scientific Reports

GEM-based computational modeling for exploring metabolic interactions in a microbial community – Soraya Mirzaei – PLoS Computational Biology

Review: Techniques, procedures, and applications in microbiome analysis – Adriana González – Advances in Genetics

June 16, 2024

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Human and General Microbiome

Mouse IgA modulates human gut microbiota with inflammatory bowel disease patients – Keishu Takahashi – Journal of Gastroenterology

Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis – Chang-Ming Chen – Journal of Translational Medicine

The microbial composition of pancreatic ductal adenocarcinoma: A systematic review of 16S rRNA gene sequencing – Nabeel Merali – International Journal of Surgery

Therapeutic microbiome modulation: new frontiers in HIV treatment – Rene Bulnes – Current Opinion in HIV and AIDS

Untargeted metabolomics reveal signatures of a healthy lifestyle – Wimal Pathmasiri – Scientific Reports

In-depth microbiological characterization of urine from subjects with type 2 diabetes – Marco Calvigioni – The Journal of Clinical Endocrinology and Metabolism

Study on intestinal parasitic infections and gut microbiota in cancer patients at a tertiary teaching hospital in Malaysia – Sidi Omar Siti Farah Norasyikeen – Scientific Reports

The vaginal microbial signatures of preterm birth woman – Huan Li – BMC Pregnancy and Childbirth

Review: Gut microbiome and cardiometabolic comorbidities in people living with HIV – Marius Trøseid – Microbiome

Review: Nontoxigenic Bacteroides fragilis: A double-edged sword – Yumei Huang – Microbiological Research

Review: Vaginal microbiota and gynecological cancers: a complex and evolving relationship – Kasra Javadi – Infectious Agents and Cancer

Review: Microbial genomics: a potential toolkit for forensic investigations – Pooja Tripathi – Forensic Science, Medicine, and Pathology

Beneficial Microbes and Compounds

Metformin-induced changes in the gut microbiome and plasma metabolome are associated with cognition in men – Marisel Rosell-Díaz – Metabolism: Clinical and Experimental

Effects of Bifidobacterium breve 207-1 on regulating lifestyle behaviors and mental wellness in healthy adults based on the microbiome-gut-brain axis: a randomized, double-blind, placebo-controlled trial – Jinxing Li – European Journal of Nutrition

Bacteria of healthy periodontal tissues as candidates of probiotics: a systematic review – María Del Pilar Angarita-Díaz – European Journal of Medical Research

Animal Model Microbiome

Investigating the influence of perinatal fluoxetine exposure on murine gut microbial communities during pregnancy and lactation – Katelyn Desorcy-Scherer – Scientific Reports

Microbiota dictate T cell clonal selection to augment graft-versus-host disease after stem cell transplantation – Albert C Yeh – Immunity

Non-Model Animal Microbiome

Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea – Lilli Ginevra – Animal Microbiome

Plant Microbiome

Plant growth promotion and biocontrol properties of a synthetic community in the control of apple disease – Rongye Qiao – BMC Plant Biology

Review: Microbial Consortia: Promising Tool as Plant Bioinoculants for Agricultural Sustainability – Rajeshwari Negi – Current Microbiology

Environmental Microbiome

Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes – Periyasamy Sivalingam – Journal of Hazardous Materials

Microbiome Analysis: Tools, Techniques and Resources

mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics – Kris Sankaran – PLoS Computational Biology

Other

Editorial: Direct-to-consumer microbiome testing needs regulation  – The Lancet Gastroenterology & Hepatology

June 2, 2024

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Human Microbiome

Commensal bacterial outer membrane protein A induces interleukin-22 production – Yanling Wang – Cell Reports

Mucus production, host-microbiome interactions, hormone sensitivity, and innate immune responses modeled in human cervix chips – Zohreh Izadifar – Nature Communications

Gut microbiome and symptoms in females with irritable bowel syndrome: a cross-sectional analysis – K J Kamp – Beneficial Microbes

Gut microbiome in the Graves’ disease: Comparison before and after anti-thyroid drug treatment – Chaiho Jeong – PloS ONE

Guild-level signature of gut microbiome for diabetic kidney disease – Shasha Tang – mBio

Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study – JooHee Choi – EClinicalMedicine

Gut microbiota-derived butyrate induces epigenetic and metabolic reprogramming in myeloid-derived suppressor cells to alleviate primary biliary cholangitis – Rui Wang – Gastroenterology

Review: Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes – Yuhao Fu – mLife

Review: Exploring the Impact of Airway Microbiome on Asthma Morbidity: A Focus on the Constructing a ‘Eubiosis Reinstatement Therapy’ for Asthma-CURE Project – Paraskevi Xepapadaki – Pulmonary Therapy

Beneficial Microbes and Compounds

A Gram-negative-selective antibiotic that spares the gut microbiome – Kristen A Muñoz – Nature

Bifidobacterium adolescentis-derived hypaphorine alleviates acetaminophen hepatotoxicity by promoting hepatic Cry1 expression – Ping Qin – Journal of Translational Medicine

Chrysanthemum morifolium attenuates metabolic and alcohol-associated liver disease via gut microbiota and PPARα/γ activation – Dan Liu – Phytomedicine

Animal Model Microbiome

Transgenerational effects of early life stress on the fecal microbiota in mice – Nize Otaru – Communications Biology

Metagenomics and metaproteomics alterations are associated with kidney disease in opisthorchiasis hamsters fed a high-fat and high-fructose diet – Keerapach Tunbenjasiri – PloS ONE

Animal Microbiome

Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats – Qingyong Hu – Applied Microbiology and Biotechnology

Interaction between methanotrophy and gastrointestinal nematodes infection on the rumen microbiome of lambs – Patricia Spoto Corrêa – FEMS Microbiology Ecology

Antibiotic-altered gut microbiota explain host memory plasticity and disrupt pace-of-life covariation for an aquatic snail – Gabrielle L Davidson – The ISME Journal

Food Microbiome

Metagenome-assembled genomes from microbiomes fermenting dairy coproducts – Kevin A Walters – Microbiology Resource Announcements

Environmental Microbiome

Global biogeography of microbes driving ocean ecological status under climate change – Zhenyan Zhang – Nature Communications

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling – Zhepu Ruan – Nature Communications

Interpretable machine learning decodes soil microbiome’s response to drought stress – Michelle Hagen – Environmental Microbiome

Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens – Natalia Timanikova – Environmental Microbiology

Microbiome Analysis

Combining compositional data sets introduces error in covariance network reconstruction – James D Brunner – ISME Communications

How to Obtain and Compare Metagenome-Assembled Genomes – Fabio Beltrame Sanchez – Methods in Molecular Biology

A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros – Fentaw Abegaz – Scientific Reports

Review: A review of machine learning methods for cancer characterization from microbiome data – Marco Teixeira – NPJ Precision Oncology

May 26, 2024

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Human Microbiome in General

Microbiome research in Africa must be based on equitable partnerships – Ovokeraye H Oduaran – Nature Medicine

Human Gut Microbiome

IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota – Ivo Röwekamp – PNAS

Meta-analysis of shotgun sequencing of gut microbiota in Parkinson’s disease – Hiroshi Nishiwaki – NPJ Parkinson’s Disease

Systematic review of associations between gut microbiome composition and stunting in under-five children – Mwelwa Chibuye – NPJ Biofilms and Microbiomes

Production of deoxycholic acid by low-abundant microbial species is associated with impaired glucose metabolism – Annika Wahlström – Nature Communications

Altered gut microbiota is associated with the formation of occult hepatitis B virus infection – Bochao Liu – Microbiology Spectrum

Metagenome-assembled genomes (MAGs) suggest an acetate-driven protective role in gut microbiota disrupted by Clostridioides difficile – Giovanny Herrera – Microbiological Research

Review: From gut microbiota to brain: implications on binge eating disorders – Weiwei Guo – Gut Microbes

Review: Pathogenesis and therapeutic opportunities of gut microbiome dysbiosis in critical illness – Nicole A Cho – Gut Microbes

Human Respiratory Tract Microbiome

Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation – Matt S Zinter – Nature Medicine

Human Genitourinary Tract Microbiome

Leveraging existing 16S rRNA gene surveys to decipher microbial signatures and dysbiosis in cervical carcinogenesis – Xiaoxiao Li – Scientific Reports

Targeting Megasphaera species to promote cervicovaginal health – Mariano A Molina – Trends in Microbiology

Beneficial Microbes and Compounds

Prodrug-conjugated tumor-seeking commensals for targeted cancer therapy – Haosheng Shen – Nature Communications

Fecal microbiota transplantation significantly improved respiratory failure of amyotrophic lateral sclerosis – Jingshuang Yan – Gut Microbes

The use of probiotics and prebiotics in decolonizing pathogenic bacteria from the gut; a systematic review and meta-analysis of clinical outcomes – Md Nannur Rahman – Gut Microbes

Review: Advanced microbiome therapeutics as a novel modality for oral delivery of peptides to manage metabolic diseases – Ruben Vazquez-Uribe – Trends in Endocrinology and Metabolism

Animal Microbiome

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis – Yujie Meng – Microbiome

Symbiotic bacteria and fungi proliferate in diapause and may enhance overwintering survival in a solitary bee – Shawn M Christensen – The ISME Journal

Plant Microbiome

Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness – Xiaofang Wang – mBio

Environmental Microbiome

Global epistasis and the emergence of function in microbial consortia – Juan Diaz-Colunga – Cell

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution – Brune Joannard – Microbiome

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome – Yoko Masuda – Microbiome

A global initiative for ecological and evolutionary hologenomics – Aoife Leonard – Trends in Ecology & Evolution

Built Environment Microbiome

Fungal diversity differences in the indoor dust microbiome from built environments on earth and in space – Nicholas Nastasi – Scientific Reports

Microbiome Analysis: Tools, Techniques and Resources

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease – Katherine Do – mSphere

A comparative study of supervised and unsupervised machine learning algorithms applied to human microbiome – E Kalluçi – La Clinica Terapeutica