Tag Archives: microbiome analysis

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 9, 2024

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Human and General Microbiome

Divergent age-associated and metabolism-associated gut microbiome signatures modulate cardiovascular disease risk – Tiange Wang – Nature Medicine

Quantifying variation across 16S rRNA gene sequencing runs in human microbiome studies – Andrew J Hoisington – Applied Microbiology and Biotechnology

Gut microbiome changes associated with chronic pancreatitis and pancreatic cancer: A systematic review and Meta-analysis – Jiaze Hong – International Journal of Surgery

Gut microbial signatures of patients with diarrhea-predominant irritable bowel syndrome and their healthy relatives – Jie Chen – Journal of Applied Microbiology

Two weeks of acarbose treatment show no effect on gut microbiome composition in patients with type 2 diabetes: a randomised, placebo-controlled, double-blind, crossover study – Niels B Dalsgaard – Endocrine Connections

A conserved inhibitory interdomain interaction regulates DNA-binding activities of hybrid two-component systems in Bacteroides – Rong Gao – mBio

Multi-omics Analysis Reveals Key Gut Microbiota and Metabolites Closely Associated with Huntington’s Disease – Shu-Xia Qian – Molecular Neurobiology

Review: Unravelling the role of intratumoral bacteria in digestive system cancers: current insights and future perspectives – Weiqin Lu – Journal of Translational Medicine

Model and Non-model Animal Microbiome

Effect of microplastics pollution on the gut microbiome of anecic and endogeic earthworms – Christina Papazlatani – FEMS Microbiology Letters

Novel indigenous probiotic isolated from healthy Pacific White shrimp Litopenaeus vannamei intestine in differing stages based on metagenomic and screening approach – Sutanti Sutanti – Fish & Shellfish Immunology

Citrobacter rodentium infection impairs dopamine metabolism and exacerbates the pathology of Parkinson’s disease in mice – Yongtao He – Journal of Neuroinflammation

Gut microbiota depletion delays somatic peripheral nerve development and impairs neuromuscular junction maturation – Matilde Cescon – Gut Microbes

Plant Microbiome

Review: Unravelling the impact of environmental factors in shaping plant microbiomes – Alicia Isabel Pérez-Lorente – Microbial Biotechnology

Microbiome Analysis

GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences – Calum J Walsh – Microbial Genomics

Machine learning enabled design features of antimicrobial peptides selectively targeting peri-implant disease progression – Kyle Boone – Frontiers in Dental Medicine

Review: An exploratory in silico analysis of bacteriocin gene clusters in the urobiome – Jennifer Jones – Microbiome Research Reports

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

May 12, 2024

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Human and General Microbiome

Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota in vitro – Jenni Firrman – mBio

HIV rebound in HIV controllers is associated with a specific fecal microbiome profile – Yanhui Cai – European Journal of Immunology

Comparative analysis of the tumor microbiome, molecular profiles, and immune cell abundances by HPV status in mucosal head and neck cancers and their impact on survival – Rituraj Upadhyay – Cancer Biology & Therapy

Metatranscriptome and resistome of the endodontic microbiome – Ericka T Pinheiro – Journal of Endodontics

Microbiome of periodontitis and peri-implantitis before and after therapy: Long-read 16S rRNA gene amplicon sequencing – Pei-Shiuan Yu – Journal of Periodontal Research

Review: Akkermansia muciniphila: a deworming partner independent of type 2 immunity – Jiaqi Wang – Gut Microbes

Review: The gut microbiome in alcohol use disorder and alcohol-associated liver disease: A systematic review of clinical studies – Erica N Grodin – Alcohol, Clinical & Experimental Research

Review: Bile acid-microbiota crosstalk in hepatitis B virus infection – Jiaxin Wang – Journal of Gastroenterology and Hepatology

Review: Ecological insights into hematopoiesis regulation: unraveling the influence of gut microbiota – Kaiwen Zheng – Gut Microbes

Review: Interactions between host and gut microbiota in gestational diabetes mellitus and their impacts on offspring – Shuxian Wang – BMC Microbiology

Beneficial Microbes and Compounds

Review: Mechanisms of microbiota modulation: Implications for health, disease, and therapeutic interventions – Okechukwu Paul-Chima Ugwu – Medicine

Lactobacillus paracasei Jlus66 relieves DSS-induced ulcerative colitis in a murine model by maintaining intestinal barrier integrity, inhibiting inflammation, and improving intestinal microbiota structure – Fazheng Yu – European Journal of Nutrition

Conjugated linoleic acid metabolite impact in colorectal cancer: a potential microbiome-based precision nutrition approach – Adriana González – Nutrition Reviews

Microbiome in Animal Models

Aging amplifies a gut microbiota immunogenic signature linked to heightened inflammation – Maria Elisa Caetano-Silva – Aging Cell

Bacteroidota inhibit microglia clearance of amyloid-beta and promote plaque deposition in Alzheimer’s disease mouse models – Caroline Wasén – Nature Communications

Prevotella copri promotes vascular calcification via lipopolysaccharide through activation of NF-κB signaling pathway – Qing-Yun Hao – Gut Microbes

Non-Model Animal Microbiome

Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure – Paul Oladele – Microbiology Spectrum

Characterizing the blood microbiota in healthy and febrile domestic cats via 16s rRNA sequencing – Liam Kitson – Scientific Reports

Plant/Rhizosphere Microbiome

Metagenomic sequencing and reconstruction of 82 microbial genomes from barley seed communities – Kalonji A Tshisekedi – Scientific Data

Modulation of rhizosphere microbial community and metabolites by bio-functionalized nanoscale silicon oxide alleviates cadmium-induced phytotoxicity in bayberry plants – Temoor Ahmed – The Science of the Total Environment

Phyllosphere fungal diversity generates pervasive nonadditive effects on plant performance – Brianna K Almeida – The New Phytologist

Environmental Microbiome

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities – Rehab Z Abdallah – mSystems

Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures – Wei Li – The ISME Journal

Genomic fingerprints of the world’s soil ecosystems – Emily B Graham – mSystems

Review: Insights into cyanobacterial blooms through the lens of omics – Ve Van Le – The Science of the Total Environment

Microbiome Analysis

fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data – Shen Zhang – Bioinformatics

Review: A Standard Pipeline for Analyzing the Endometrial Microbiome – Mychelle de Medeiros Garcia Torres – Reproductive Sciences 

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 21, 2024

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Human and General Microbiome

Mechanoelectronic stimulation of autologous extracellular vesicle biosynthesis implant for gut microbiota modulation – Shuangshuang Wan – Nature Communications

Oral bacterial insights from a comparative study between healthy and comorbid diseased human individuals – Anand Ravichandran – Microbial Pathogenesis

Dietary fiber guar gum-induced shift in gut microbiota metabolism and intestinal immune activity enhances susceptibility to colonic inflammation – Devendra Paudel – Gut Microbes

Highly specific vaginal microbiome signature for gynecological cancers – Mengzhen Han – Open Life Sciences

Incretin hormones, obesity and gut microbiota – Giulia Angelini – Peptides

Review: Role of imbalanced gut microbiota in promoting CRC metastasis: from theory to clinical application – Shiying Fan – Cell Communication and Signaling

Review: The Role of the Gut Microbiome in Health and Disease in the Elderly – Lea Ann Chen – Current Gastroenterology Reports

Review: Application of Microbiome-Based Therapies in Chronic Respiratory Diseases – Se Hee Lee – Journal of Microbiology

Review: Apical root canal microbiome associated with primary and posttreatment apical periodontitis: A systematic review – José F Jr Siqueira – International Endodontic Journal

Review: An insider’s perspective about the pathogenic relevance of gut bacterial transportomes – Hassan Zafar – Microbial Physiology

Beneficial Microbes and Compounds

Butyrate as a potential therapeutic agent for neurodegenerative disorders – Prapti Chakraborty – Neurochemistry International

Adherence to the Mediterranean diet can beneficially affect the gut microbiota composition: a systematic review – Armin Khavandegar – BMC Medical Genomics

Food Microbiome

Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider – Ignat V Sonets – Food Microbiology

New evidence for gut-muscle axis: Lactic acid bacteria-induced gut microbiota regulates duck meat flavor – Ligen Xu – Food Chemistry

Animal Microbiome

Safety evaluation and effects of dietary phlorotannins on the growth, health, and intestinal microbiota of Litopenaeus vannamei – Zijie Wu – Fish & Shellfish Immunology

A longitudinal study of queen health in honey bees reveals tissue specific response to seasonal changes and pathogen pressure – Duan C Copeland – Scientific Reports

The microbiome of a Pacific moon jellyfish Aurelia coerulea – Aki H Ohdera – PloS one

Plant Microbiome

The rhizosphere and root selections intensify fungi-bacteria interaction in abiotic stress-resistant plants – Feng Huang – PeerJ

Environmental Microbiome

Exploring microbiome and plankton responses and interactions in the mangrove ecosystem through eDNA and network analysis – Jie Meng – The Science of the Total Environment

Quantifying genome specific carbon fixation in a 750 meter deep subsurface hydrothermal microbial community – Ömer K Coskun – FEMS Microbiology Ecology

Microbiome Analysis

A generic approach to infer community-level fitness of microbial genes – Teng Wang – PNAS

Randomized feature selection based semi-supervised latent Dirichlet allocation for microbiome analysis – Namitha Pais – Scientific Reports

Review: Deep learning methods in metagenomics: a review – Gaspar Roy – Microbial Genomics