Tag Archives: beneficial microbes

November 3, 2024

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Human and General Microbiome

Gut microbiota and metabolic profile changes unveil the deterioration of alveolar bone inflammatory resorption with aging induced by D-galactose – Fangzhou Liu – Scientific Reports

The human gut symbiont Ruminococcus gnavus displays strain-specific exopolysaccharides modulating the host immune response – Victor Laplanche – Carbohydrate Polymers

Stage dependent microbial dynamics in hepatocellular carcinoma and adjacent normal liver tissues – Hee Eun Jo – Scientific Reports

Intestinal microflora and metabolites affect the progression of acute pancreatitis (AP) – Zhenjiang Wang – Gut Pathogens

Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients – Angeli D G Macandog – Cell Host & Microbe

Review: A pathophysiologic framework for the overlap of disorders of gut-brain interaction and the role of the gut microbiome – Ayesha Shah – Gut Microbes

Review: AI in microbiome-related healthcare – Niklas Probul – Microbial Biotechnology

Review: The oncomicrobiome: new insights into microorganisms in cancer – Yingying Ma – Microbial Pathogenesis

Viewpoint: Gut microbiome: a biomedical revolution – Maria Carmen Collado – Nature Reviews Gastroenterology & Hepatology

Research Highlight: Microbiome-colonizing RNAs – Andrea Du Toit – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Effects of Limosilactobacillus reuteri DSM 17938 in neonates exposed to antibiotics: a randomised controlled trial – J Lozar Krivec – Beneficial Microbes

Lactobacillus rhamnosus 1.0320 Postbiotics Ameliorate Dextran Sodium Sulfate-Induced Colonic Inflammation and Oxidative Stress by Regulating the Intestinal Barrier and Gut Microbiota – Jing Zhang – Journal of Agricultural and Food Chemistry

Oral administration of Lactobacillus casei DG® after ileostomy closure in restorative proctocolectomy: a randomized placebo-controlled trial (microbiota and immune microenvironment in pouchitis -MEP1) – Imerio Angriman – Gut Microbes

Development of interleukin-27 recombinant Lactococcus lactis and its efficacy in treating psoriasis and colitis in mice – Shaoju Qian – International Journal of Biological Macromolecules

Animal Models

The gut microbiome in patients with Cushing’s disease affects depression- and anxiety-like behavior in mice – Ding Nie – Microbiome

Alpha-synuclein overexpression and the microbiome shape the gut and brain metabolome in mice – Livia H Morais – NPJ Parkinson’s Disease

Transfer of microbiota from lean donors in combination with prebiotics prevents excessive weight gain and improves gut-brain vagal signaling in obese rats – Dulce M Minaya – Gut Microbes

Animal Microbiome (non-models)

Microbiome divergence of marine gastropod species separated by the Isthmus of Panama – Alexander T Neu – Applied and Environmental Microbiology

Plant and Soil Microbiome

Planting density effect on poplar growth traits and soil nutrient availability, and response of microbial community, assembly and function – Rongye Qiao – BMC Plant Biology

Plant growth-promoting fungi improve tobacco yield and chemical components by reassembling rhizosphere fungal microbiome and recruiting probiotic taxa – Mingzi Shi – Environmental Microbiome

Review: Community standards and future opportunities for synthetic communities in plant-microbiota research – Trent R Northen – Nature Microbiology

Review: Alpine and subalpine plant microbiome mediated plants adapt to the cold environment: A systematic review – Mengyan Hou – Environmental Microbiome

Environmental Microbiome

Arctic’s hidden hydrocarbon degradation microbes: investigating the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on microbial communities and hydrocarbon biodegradation pathways in high-Arctic beaches – Ya-Jou Chen – Environmental Microbiome

SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas – Lei Gao – Microbial Ecology

Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach – Maryem Wardi – Scientific Reports

Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome – Arunmozhi Bharathi Achudhan – World Journal of Microbiology & Biotechnology

October 20, 2024

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Human and General Microbiome

Fecal glycoprotein 2 is a marker of gut microbiota dysbiosis and systemic inflammation – Fabian Frost – Gut Pathogens

Detrimental effect of an early exposure to antibiotics on the outcomes of immunotherapy in a multi-tumor cohort of patients – Patricia Guerrero – The Oncologist

Upper respiratory microbial communities of healthy populations are shaped by niche and age – Susan Zelasko – Microbiome

Dysbiosis of the initial stool microbiota increases the risk of developing necrotizing enterocolitis or feeding intolerance in newborns – Hyojin Chae – Scientific Reports

Resource sharing of an infant gut microbiota synthetic community in combinations of human milk oligosaccharides – Athanasia Ioannou – The ISME Journal

Aging-induced dysbiosis worsens sepsis severity but is attenuated by probiotics in D-galactose-administered mice with cecal ligation and puncture model – Chalisa Pinitchun – PloS One

Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury – Fan Lu – Microbiology Spectrum

A Blautia producta specific gFET-based aptasensor for quantitative monitoring of microbiome quality – Hu Xing – Nanoscale Horizons

Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery – Celia Boukadida – Microbiome

Review: Gut microbiota determines the fate of dietary fiber-targeted interventions in host health – Wenjing Wang – Gut Microbes

Beneficial Microbes and Compounds

Vaginal lactobacilli produce anti-inflammatory β-carboline compounds – Virginia J Glick – Cell host & Microbe

EphA2 blockage ALW-II-41-27 alleviates atherosclerosis by remodeling gut microbiota to regulate bile acid metabolism – Cong Lu – NPJ Biofilms and Microbiomes

Lactobacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB-12 promote infected wound healing via regulation of the wound microenvironment – Zhe Yin – Microbial Biotechnology

Ameliorative effects of Akkermansia muciniphila on anxiety-like behavior and cognitive deficits in a rat model of Alzheimer’s disease – Hamideh Maftoon – Brain Research

Animal Microbiome

Bacterial and Symbiodiniaceae communities’ variation in corals with distinct traits and geographical distribution – Livia Bonetti Villela – Scientific Reports

The Role of Geography, Diet, and Host Phylogeny on the Gut Microbiome in the Hawaiian Honeycreeper Radiation – Maria S Costantini – Ecology and Evolution

New insights into the enteric methane production based on the archaeal genome map of ruminant gastrointestinal tract – Yifan Tang – Journal of Advanced Research

Plant and Soil Microbiome

A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants – Alon Avraham Ginatt – eLife

Unravelling the microbiome of wild flowering plants: a comparative study of leaves and flowers in alpine ecosystems – Dinesh Kumar Ramakrishnan – BMC Microbiology

Algae-fungi symbioses and bacteria-fungi co-exclusion drive tree species-specific differences in canopy bark microbiomes – Jule Freudenthal – The ISME Journal

Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning – Yujie Mo – Communications Biology

More Microbes

Community successional patterns and inter-kingdom interactions during granular biofilm development – Miguel de Celis – NPJ Biofilms and Microbiomes

Metagenome-based microbial community analysis of urine-derived fertilizer – Nebiyat N Woldeyohannis – BMC Microbiology

Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters – Natchapon Srinak – PLoS Computational Biology

Microbiome Analysis: Tools, Techniques and Resources

Evaluation of inter- and intra-variability in gut health markers in healthy adults using an optimised faecal sampling and processing method – Kirsten Kruger – Scientific Reports

LineageFilter: Improved Proteotyping of Complex Samples Using Metaproteomics and Machine Learning – Hamid Hachemi – Journal of Proteome Research

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 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 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

May 5, 2024

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Human and General Microbiome

Paternal microbiome perturbations impact offspring fitness – Ayele Argaw-Denboba – Nature

Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes – Chen Liao – Nature Microbiology

Human gut microbiota and their production of endocannabinoid-like mediators are directly affected by a dietary oil – Charlène Roussel – Gut Microbes

Leveraging genomic signatures of oral microbiome-associated antibiotic resistance genes for diagnosing pancreatic cancer – Xiaojing Shen – PloS ONE

Deciphering the Pancreatic Cancer Microbiome in Mainland China: Impact of Exiguobacterium/Bacillus ratio on Tumor Progression and Prognostic Significance – Zhengyan Zhang – Pharmacological Research

Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism – Xianyi Xiong – The ISME Journal

Microplastics and microbiota: Unraveling the hidden environmental challenge – Jean Demarquoy – World Journal of Gastroenterology

Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus – Emilene Da Silva Morais – Scientific Reports

Review: A catalog of ethanol-producing microbes in humans – Babacar Mbaye – Future Microbiology

Review: Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review – Madjid Morsli – Annals of Clinical Microbiology and Antimicrobials

Beneficial Microbes

A consortium of Hordeum vulgare and gut microbiota against non-alcoholic fatty liver disease via data-driven analysis – Su-Been Lee – Artificial Cells, Nanomedicine, and Biotechnology

Animal Microbiome

Amphibian tolerance to arsenic: microbiome-mediated insights – Isabella Ferreira Cordeiro – Scientific Reports

Combined effect of seasons and life history in an anuran strengthens the response and relationship between their physiology and gut microbiota – Jun-Kyu Park – Scientific Reports

Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments – Judith Guitart-Matas – Animal Microbiome

Effects of microbiome transplants on fly microbiome – Jorge Ferreira – Lab Animal

Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China – Hongjin Liu – Integrative Zoology

Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing – Edwin Omar Rivera-Lopez – Data in Brief

Plant Microbiome

Depletion of protective microbiota promotes the incidence of fruit disease – Xue Luo – The ISME Journal

Analysis of Salt Stress on Soil Microbial Community Composition and Its Correlation with Active Components in the Rhizosphere of Acanthopanax senticosus – Wenhui Yuan – Current Microbiology

Environmental Microbiome

Mechanisms and implications of bacterial-fungal competition for soil resources – Chaoqun Wang – The ISME Journal

Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments – Ye Chen – Microbiology Spectrum

Microbiome Analysis

mbDecoda: a debiased approach to compositional data analysis for microbiome surveys – Yuxuan Zong – Briefings in Bioinformatics

EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale – Sunil Nagpal – Microbiology Spectrum

mi-Mic: a novel multi-layer statistical test for microbiota-disease associations – Oshrit Shtossel – Genome Biology

Review: Unveiling microbial diversity: harnessing long-read sequencing technology – Daniel P Agustinho – Nature Methods

April 28, 2024

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Human and General Microbiome

Genome Analysis of Epsilon CrAss-like Phages – Igor V Babkin – Viruses

Cervical microbiota dysbiosis associated with high-risk Human Papillomavirus infection – Natalia Zeber-Lubecka – PloS ONE

Association of the trimethylamine N-oxide with cardiovascular risk and vascular alterations in middle-aged patients with risk factors for cardiovascular diseases – Natalia Spasova – Bioscience Reports

Insights into microorganisms, associated factors, and the oral microbiome in infective endocarditis patients – Ayden Ismail – Frontiers in Oral Health

Alterations in the fecal microbiota of methamphetamine users with bad sleep quality during abstinence – Zijing Deng – BMC Psychiatry

Gut microbiome predicts cognitive function and depressive symptoms in late life – A Kolobaric – Molecular Psychiatry

Microbial signatures in human periodontal disease: a metatranscriptome meta-analysis – Armen Ovsepian – Frontiers in Microbiology

Gut microbiome composition reveals the distinctiveness between the Bengali people and the Indigenous ethnicities in Bangladesh – Ishtiaque Ahammad – Communications Biology

Comparative analysis of endometrial, vaginal, and gut microbiota in patients with and without adenomyosis – Marta Valdés-Bango – Acta Obstetricia et Gynecologica Scandinavica

Causal effect of gut microbiota and diabetic nephropathy: a Mendelian randomization study – Ganyuan He – Diabetology & Metabolic Syndrome

The characteristics of microbiome in the upper respiratory tract of COVID-19 patients – Xilong Zhang – BMC Microbiology

Review: Interplay of human gastrointestinal microbiota metabolites: Short-chain fatty acids and their correlation with Parkinson’s disease – Jiaji Liu – Medicine

Review: Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery – Saumitra Sengupta – Organic & Biomolecular Chemistry

Review: Oligella spp.: A systematic review on an uncommon urinary pathogen – Eric Farfour – European Journal of Clinical Microbiology & Infectious Diseases

Review: The potential importance of the built-environment microbiome and its impact on human health – Thomas C G Bosch – PNAS

Beneficial Microbes and Compounds

Vitamin D regulates microbiome-dependent cancer immunity – Evangelos Giampazolias – Science 

HMOs Impact the Gut Microbiome of Children and Adults Starting from Low Predicted Daily Doses – Danica Bajic – Metabolites

Effects of microbiome-based interventions on neurodegenerative diseases: a systematic review and meta-analysis – Zara Siu Wa Chui – Scientific Reports

A randomized, double-blinded, placebo-controlled clinical trial on Lactobacillus-containing cultured milk drink as adjuvant therapy for depression in irritable bowel syndrome – Marlynna Sarkawi – Scientific Reports

Animal Microbiome

Review: Understanding the Diversity and Roles of the Ruminal Microbiome – Gi Beom Keum – Journal of Microbiology

Plant Microbiome

Impacts of continuous cropping on the rhizospheric and endospheric microbial communities and root exudates of Astragalus mongholicus – Qin Zhou – BMC Plant Biology

Comparative analysis of root associated microbes in tropical cultivated and weedy rice (Oryza spp.) and temperate cultivated rice – Vani Juliyanti – Scientific Reports

Identifying causes and consequences of rhizosphere microbiome heritability – Maggie R Wagner – PLoS Biology

Environmental Microbiome

Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus ‘Igneacidithiobacillus’ – Dilanaz Arisan – Frontiers in Microbiology

Exploring changes in microplastic-associated bacterial communities with time, location, and polymer type in Liusha Bay, China – Ting Wang – Marine Environmental Research

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface – Jennifer L Goff – Environmental Microbiome

Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench – Yan-Ru Dang – Microbiome

Microbiome Analysis

Microbiome compositional data analysis for survival studies – Meritxell Pujolassos – NAR Genomics and Bioinformatics

Other

Periportal macrophages protect against commensal-driven liver inflammation – Yu Miyamoto – Nature

A case study to engage students in the research design and ethics of high-throughput metagenomics – Courtney Carroll Alexander – Journal of Microbiology & Biology Education

April 7, 2024

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Human and General Microbiome

The secreted protein Amuc_1409 from Akkermansia muciniphila improves gut health through intestinal stem cell regulation – Eun-Jung Kang – Nature Communications

A universal plasma metabolites-derived signature predicts cardiovascular disease risk in MAFLD – Zhonglin Li – Atherosclerosis

Oral-gut microbial transmission promotes diabetic coronary heart disease – Yiwen Li – Cardiovascular Diabetology

Comparative analysis of microbial composition and functional characteristics in dental plaque and saliva of oral cancer patients – Man Zhang – BMC Oral Health

Investigating the causal role of the gut microbiota in esophageal cancer and its subtypes: a two-sample Mendelian randomization study – Jia Li – BMC Cancer

Beneficial Microbes and Compounds

Gut bacteria-driven homovanillic acid alleviates depression by modulating synaptic integrity – Mingliang Zhao – Cell Metabolism

Animal Microbiome (model and non-model)

Stress-induced mucin 13 reductions drive intestinal microbiome shifts and despair behaviors – Courtney R Rivet-Noor – Brain, Behavior, and Immunity

Integrated analysis of intestinal microbiota and transcriptome reveals that a coordinated interaction of the endocrine, immune system and gut microbiota response to heat stress in Litopenaeus vannamei – Guowei Liao – Developmental and Comparative Immunology

Associations between the rumen microbiota and carcass merit and meat quality in beef cattle – Devin B Holman – Applied Microbiology and Biotechnology

Characterization of oral microbiota in 6-8-month-old small breed dogs – Masahiro Morita – BMC Veterinary Research

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments – Yingjian Wu – Microbiome

Effects of fecal microbiota transfer on blood pressure in animal models: A systematic review and meta-analysis – Lingyu Lin – PloS ONE

Zoonotic bacteria in the vicinity of animal farms as a factor disturbing the human microbiome: a review – Anna Kozajda – International Journal of Occupational Medicine and Environmental Health

Metagenomic insights into jellyfish-associated microbiome dynamics during strobilation – Saijun Peng – ISME Communications

Host evolution shapes gut microbiome composition in Astyanax mexicanus – Misty R Riddle – Ecology and Evolution

Environmental Microbiome

Heavy metal induced shifts in microbial community composition and interactions with dissolved organic matter in coastal sediments – Yu Wang – The Science of the Total Environment

Long-term and combined heavy-metal contamination forms a unique microbiome and resistome: A case study in a Yellow River tributary sediments – Yu Cao – Environmental Research

Deciphering the impact of cold-adapted bioinoculants on rhizosphere dynamics, biofortification, and yield of kidney bean across varied altitudinal zones – Amir Khan – The Science of the Total Environment

Plant Microbiome

Analysis of microbial dynamics in the soybean root-associated environments from community to single-cell levels – Masako Kifushi – Journal of Bioscience and Bioengineering

Microbiome Analysis: Tools, Protocols, Techniques and Resources

phylaGAN: Data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data – Divya Sharma – Bioinformatics

March 31, 2024

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Human Microbiome

The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children – Sarah M Heston – Gut Microbes

Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung – Patrick J Dörner – Nature Communications

The gut metabolite indole-3-propionic acid activates ERK1 to restore social function and hippocampal inhibitory synaptic transmission in a 16p11.2 microdeletion mouse model – Jian Jiang – Microbiome

Vaginal microbiomes of breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms – Pimpun Prasanchit – Scientific Reports

Integrated analysis of gut metabolome, microbiome, and brain function reveal the role of gut-brain axis in longevity – Bin Jiao – Gut Microbes

Exploring the diversity of vaginal microbiota between healthy women and cervical cancer patients in India – Ashwini Kamble – Journal of Medical Microbiology

Oral pathobiont Klebsiella chaperon usher pili provide site-specific adaptation for the inflamed gut mucosa – Yijie Guo – Gut Microbes

Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut – Yi Han Tan – The ISME Journal

Review: Microbiome bacterial influencers of host immunity and response to immunotherapy – Yeganeh Yousefi – Cell Reports. Medicine

Beneficial Microbes

Review: Unlocking the Potential of Probiotics: A Comprehensive Review on Research, Production, and Regulation of Probiotics – Tales Fernando da Silva – Probiotics and Antimicrobial Proteins

Mulberry leaf and konjac flour compound dietary fiber improves digestion and metabolism in elderly mice with high-fish-protein diet by regulating gut microbiota structure and intestinal tissue repair – Liling Deng – Food Chemistry: X

Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes – Zheng Wang – Circulation Research

Animal Microbiome (model and non-model)

Colitis reduces active social engagement in mice and is ameliorated by supplementation with human microbiota members – D Garrett Brown – Nature Communications

Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont – Alexander Harry McGrath – NPJ Biofilms and Microbiomes

Microplastics dampen the self-renewal of hematopoietic stem cells by disrupting the gut microbiota-hypoxanthine-Wnt axis – Lingli Jiang – Cell Discovery

Review: Immune interactions between mosquitoes and microbes during midgut colonization – Julia A Cai – Current Opinion in Insect Science

Microbiome Analysis

A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts – Jie Pan – Briefings in Bioinformatics

Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes – Zhanshan Sam Ma – BMC Bioinformatics

An in-depth evaluation of metagenomic classifiers for soil microbiomes – Niranjana Rose Edwin – Environmental Microbiome

Generalized reporter score-based enrichment analysis for omics data – Chen Peng – Briefings in Bioinformatics