Tag Archives: Microbiome Digest

November 17, 2024

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Human and General Microbiome

F. prausnitzii potentially modulates the association between citrus intake and depression – Chatpol Samuthpongtorn – Microbiome

Perturbations in the airway microbiome are associated with type 2 asthma phenotype and severity – Wei Zhang – Annals of Allergy, Asthma & Immunology

Altered intestinal microbiota and fecal metabolites in patients with latent and active pulmonary tuberculosis – Hua Zhang – Tuberculosis

Mendelian randomization analyses support causal relationships between gut microbiome and longevity – Shu Chen – Journal of Translational Medicine

Natal factors influencing newborn’s oral microbiome diversity – Yoon-Hee Kim – Scientific Reports

Age-related loss of intestinal barrier integrity plays an integral role in thymic involution and T cell ageing – Jessica Conway – Aging Cell

Early-life Upper Airway Microbiota are Associated with Decreased Lower Respiratory Tract Infections – Susan Zelasko – The Journal of Allergy and Clinical Immunology

Human Milk Microbiome Is Associated With Allergic Diseases in Early Childhood – Jie Ma – Allergy

Faecal microbiota composition and impulsivity in a cohort of older adults with metabolic syndrome – Prokopis Konstanti – Scientific Reports

Microbiota-induced alteration of kynurenine metabolism in macrophages drives formation of creeping fat in Crohn’s disease – Jinjie Wu – Cell Host & Microbe

Review: Estimates of microbiome heritability across hosts – Andrew H Morris – Nature Microbiology

Beneficial Microbes and Compounds

High barley intake in non-obese individuals is associated with high natto consumption and abundance of butyrate-producing bacteria in the gut: a cross-sectional study – Satoko Maruyama – Frontiers in Nutrition

Review: Prebiotics in food and dietary supplements: a roadmap to EU health claims – Kieran Tuohy – Gut Microbes

Animal Models

The Microbiome Modifies Manifestations of Hemophagocytic Lymphohistiocytosis in Perforin-Deficient Mice – Jasmin Mann – European Journal of Immunology

Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut – Guillaume Urtecho – Cell Systems

Non-Model Animal Microbiome

Multi-omics investigation into long-distance road transportation effects on respiratory health and immunometabolic responses in calves – Jiancheng Qi – Microbiome

Plant and Soil Microbiome

Wild again: recovery of a beneficial Cannabis seed endophyte from low domestication genotypes – Carolina Lobato – Microbiome

Trade-offs and adaptation to metalliferous soils: The role of soil microbiome in metal tolerance and uptake in Arabidopsis halleri ecotypes from a reciprocal transplant experiment – Priyanka Kushwaha – The Science of the Total Environment

Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better – Tingting Wang – Microbiome

Environmental Microbiome

Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing – Anxo Méndez – Journal of Photochemistry and Photobiology (B, Biology)

Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation – Lukuan Huang – Microbiome

Other Microbes

Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays – Victoria de la Sovera – Applied Microbiology and Biotechnology

Microbiome Analysis: Tools, Procedures and Resources

Faecal sample storage without ethanol for up to 24 h followed by freezing performs better than storage with ethanol for shotgun metagenomic microbiome analysis in patients with inflammatory and non-inflammatory intestinal diseases and healthy controls – Ida Marie Bruun Grønbæk – BMC Research Notes

HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors – Jiaying Li – Molecular Ecology Resources

Comparison of commonly used software pipelines for analyzing fungal metabarcoding data – Theresa Rzehak – BMC Genomics

MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies – Aidan Foo – PLoS Biology

November 14, 2024

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General human microbiome

Mapping the gut microbial structural variations in healthy aging within the Chinese population – Shen et al. Cell Reports

Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies – Killberg et al. The Lancet Microbe

[Correspondence related to the above article] Reassessing the role of butyrate-producing bacteria in infection risk – Parsanathan. The Lancet Microbe

Microbiome science of human excrement composting – Meilander & Caporaso. ISME

Microbiota-derived lysophosphatidylcholine alleviates Alzheimer’s disease pathology via suppressing ferroptosis – Zha et al. Cell Metabolism

Probiotics

Probiotics and their metabolite spermidine enhance IFN-γ+CD4+ T cell immunity to inhibit hepatitis B virus – Wang et al. Cell Reports Medicine

Virome

The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission – Majzoub et al. Nature Communications

Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions – Du et al. ISME

Bioinformatics & metagenomics

mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data – Tan et al. Briefings in Bioinformatics. 

AMRColab – a user-friendly antimicrobial resistance detection and visualization tool – Lam et al. Microbial Genomics

Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections – Benoit et al. Nature Medicine

November 10, 2024

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Human and General Microbiome

Novel biomarkers for hepatocellular carcinoma detection and treatment – Hongyuan Yi – Hepatobiliary Surgery and Nutrition

Animal Model Experiments

Gut microbiota modulates depressive-like behaviors induced by chronic ethanol exposure through short-chain fatty acids – Hui Shen – Journal of Neuroinflammation

Host genetics and gut microbiota influence lipid metabolism and inflammation: potential implications for ALS pathophysiology in SOD1(G93A) mice – Elena Niccolai – Acta Neuropathologica Communications

Lactobacillus rhamnosus modulates murine neonatal gut microbiota and inflammation caused by pathogenic Escherichia coli – Hao Xuan – BMC Microbiology

Animal Microbiome

Introduction into natural environments shifts the gut microbiome of captivity-raised filter-feeding bivalves – Stephanie N Vaughn – ISME Communications

A metagenomic catalogue of the ruminant gut archaeome – Jiandui Mi – Nature Communications

Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates – Bo Xu – NPJ Biofilms and Microbiomes

Diet affects reproductive development and microbiota composition in honey bees – Anjali Zumkhawala-Cook – Animal Microbiome

Plant Microbiome

Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis – Hamed Azarbad – ISME Communications

Can microbiome adaptations protect crops from pests and climate change? – Carolyn Beans – PNAS

Environmental Microbiome

Ecological roles of nano-picoplankton in stratified waters of an embayment in the southern Benguela – Nicole R Dames – FEMS Microbiology Letters

Metagenomic insights into inhibition of soil microbial carbon metabolism by phosphorus limitation during vegetation succession – Haocai Wang – ISME Communications

Microbiome Analysis

Cross-comparison of gut metagenomic profiling strategies – Gábor Gulyás – Communications Biology

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

November 1, 2024

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General human microbiome

[Review] Examining the healthy human microbiome concept – Joos et a. Nature Reviews Microbiology

Bifidobacteria with indole-3-lactic acid-producing capacity exhibit psychobiotic potential via reducing neuroinflammation – Qian et al. Cell Reports Medicine

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

Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn’s disease – Hacker et al. Cell Host & Microbe

Identification of gut microbiome features associated with host metabolic health in a large population-based cohort – Keshet & Segal. Nature Communications

Probiotics

Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome – Whelan et al. Nature Microbiology

Virome

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information – Gaborieau et al. Nature Microbiology

Bioinformatics

BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata – Fenske et al. Microbial Genomics

A long-context language model for deciphering and generating bacteriophage genomes – Shao and Yan. Nature Communications

Non Microbiome Piks

We continue to learn more about the mechanisms underpinning long COVID in recent weeks 

Blood transcriptomic analyses do not support SARS-CoV-2 persistence in patients with post-COVID-19 condition with chronic fatigue syndrome – Rahmati et al. The Lancet Microbe

Post-acute sequelae of SARS-CoV-2 cardiovascular symptoms are associated with trace-level cytokines that affect cardiomyocyte function – Sinclair et al. Nature Microbiology

October 27, 2024

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Human and General Microbiome

Gut

A human gut Faecalibacterium prausnitzii fatty acid amide hydrolase – Jiye Cheng – Science

A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont – Madeline L Sheahan – Science

Exploring alterations of gut/blood microbes in addressing iron overload-induced gut dysbiosis and cognitive impairment in thalassemia patients – Kanokphong Suparan – Scientific Reports

Effects of bile acids on the growth, composition and metabolism of gut bacteria – Yi-Lei Peng – NPJ Biofilms and Microbiomes

Gut-first Parkinson’s disease is encoded by gut dysbiome – Mário F Munoz-Pinto – Molecular Neurodegeneration

Metaproteomics reveals diet-induced changes in gut microbiome function according to Crohn’s disease location – Stefano Levi Mortera – Microbiome

Review: Examining the healthy human microbiome concept – Raphaela Joos – Nature Reviews Microbiology

Review: Host-pathobiont interactions in Crohn’s disease – Roberta Caruso – Nature Reviews Gastroenterology & Hepatology

Early Microbiome

Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy – Samuel S Minot – Gut Microbes

Metal availability shapes early life microbial ecology and community succession – Joshua Soto Ocaña – mBio

Virome

Oral reovirus reshapes the gut microbiome and enhances antitumor immunity in colon cancer – Won Suk Lee – Nature Communications

Oral Cavity

Pooled analysis of oral microbiome profiles defines robust signatures associated with periodontitis – Assem Soueidan – mSystems

Animal Microbiome (Model and Non-Model Organisms)

Type VI secretion systems promote intraspecific competition and host interactions in a bee gut symbiont – Erick V S Motta – PNAS

Gut bacteria facilitate leaf beetles in adapting to dietary specialization by enhancing larval fitness – Meiqi Ma – NPJ Biofilms and Microbiomes

The dietary effects of two strain probiotics (Leuconostoc mesenteroides, Lactococcus lactis) on growth performance, immune response and gut microbiota in Nile tilapia (Oreochromis niloticus) – Assel Paritova – PloS One

Effects of Lactiplantibacillus plantarum CBT LP3 and Bifidobacterium breve CBT BR3 supplementation on weight loss and gut microbiota of overweight dogs – Jihee Choi – Scientific Reports

Maternal gastrointestinal microbiome shapes gut microbial function and resistome of newborns in a cow-to-calf model – Yimin Zhuang – Microbiome

Integrated analysis of metabolome and microbiome in a rat model of perimenopausal syndrome – Yanqiu Wei – mSystems

Maternal dysbiosis produces long-lasting behavioral changes in offspring – Jacob Hudobenko – Molecular Psychiatry

DNA metabarcoding analyses reveal fine-scale microbiome structures on Western Canadian bat wings – Chadabhorn Insuk – Microbiology Spectrum

Plant and Environmental Microbiome

Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring – Nibendu Mondal – PloS One

Metagenome-assembled genomes of Macrocystis-associated bacteria – Emily G Aguirre – Microbiology Resource Announcements

Metagenomic time-series reveals a western English Channel viral community dominated by members with strong seasonal signals – Luis M Bolaños – The ISME Journal

Volatile-mediated interspecific plant interaction promotes root colonization by beneficial bacteria via induced shifts in root exudation – Xingang Zhou – Microbiome

Other Microbes

Microbial community acclimation during anaerobic digestion of high-oil food waste – Yangqing Hu – Scientific Reports

The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments – Sarah E Daly – mSystems

Microbiome Analysis: Tools, Techniques and Resources

A single-stranded based library preparation method for virome characterization – Xichuan Zhai – Microbiome

Microbiome-based correction for random errors in nutrient profiles derived from self-reported dietary assessments – Tong Wang – Nature Communications

Fecal samples and rectal swabs adequately reflect the human colonic luminal microbiota – Julia Rode – Gut Microbes

Optimal 16S rRNA gene amplicon sequencing analysis for oral microbiota to avoid the potential bias introduced by trimming length, primer, and database – Takahiko Nagai – Microbiology Spectrum

Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics – Franziska Singer – Methods in Molecular Biology

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

October 13, 2024

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Human and General Microbiome

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

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

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

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

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

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

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

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

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

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

Cancer Research

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

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

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

Beneficial Microbes and Compounds

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

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

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

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

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

Animal Microbiome

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

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

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

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

Plant Microbiome

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

Environmental Microbiome

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

Microbiome Analysis: Tools, Techniques and Resources

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

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

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

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

October 6, 2024

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Human and General Microbiome

Noninvasive, microbiome-based diagnosis of inflammatory bowel disease – Jiaying Zheng – Nature Medicine

Advancing microbiome research in Māori populations: insights from recent literature exploring the gut microbiomes of underrepresented and Indigenous peoples – Ella T Silk – mSystems

Salivary microbiota reflecting changes in subgingival microbiota – Jae-Suk Jung – Microbiology Spectrum

Differences in the human gut microbiota with varying depressive symptom severity scores – Yuka Masamura – Bioscience of Microbiota, Food and Health

Review: Sophorolipid: An Effective Biomolecule for Targeting Microbial Biofilms – Sunidhi Dhadwal – Current Microbiology

News: Microbiome-based treatment helps ease severe malnutrition – Elizabeth Pennisi – Science

Beneficial Microbes and Compounds

A multivalent mRNA-LNP vaccine protects against Clostridioides difficile infection – Mohamad-Gabriel Alameh – Science

Safety and Tolerability of CP101, a full spectrum, oral microbiome therapeutic for the prevention of recurrent C. difficile infection: A Phase 2 Randomized Controlled Trial – Jessica R Allegretti – Gastroenterology

Animal Microbiome

Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection – María Dolores Ramos-Barbero – The ISME Journal

Structural and functional differences of gut microbiota in Pomacea canaliculata from different geographical locations and habitats – Miao Fang – Ecology and Evolution

Plant Microbiome

Rhizosphere microbial community structure in high-producing, low-input switchgrass families – Christina Stonoha-Arther – PloS One

Dynamic alterations and ecological implications of rice rhizosphere bacterial communities induced by an insect-transmitted reovirus across space and time – Nan Wu – Microbiome

Microbiome Analysis: Tools, Techniques and Resources 

Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing – Zihe Xu – Cell Reports

rRNA operon improves species-level classification of bacteria and microbial community analysis compared to 16S rRNA – Sohyoung Won – Microbiology Spectrum

ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies – Andrea Fasolo – PloS One

October 2, 2024

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Gut Microbiome

Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants – Brandon Hickman et al – Nature Communications

Pangenomes of human gut microbiota uncover links between genetic diversity and stress response – Saar Shoer et al – Cell Host & Microbe

[MINI REVIEW] The human gut microbiome in health and disease: time for a new chapter? – Jee-Yon Lee et al – ASM Infection & Immunity

Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities – Amin Valiei et al – NPJ Biofilms & Microbiomes

A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases – Wen Sun et al – NPJ Biofilms & Microbiomes

A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome – Tetsuro Kawano-Sugaya et al – BMC Microbiome

Stratification of human gut microbiomes by succinotype is associated with inflammatory bowel disease status – Laura Anthamatten et al – BMC Microbiome

Impact of complementary feeding on infant gut microbiome, metabolites and early development – Yudong Shi et al – Food & Function

Can longer lifespan be associated with gut microbiota involvement in lipid metabolism? – Sára Šardzíková et al – FEMS Microbiology Ecology

Beneficial microbes & compounds

[REVIEW] Preventive effect of probiotics on oral mucositis induced by anticancer therapy: a systematic review and meta-analysis of randomized controlled trials – Bo Yang et al – BMC Oral Health

Animal Microbiome

Bacteria from the Amycolatopsis genus associated with a toxic bird secrete protective secondary metabolites – Elena Seibel et al – Nature Communications

Impact of virginiamycin on the ruminal microbiota of feedlot cattle – Bruna Parapinski Santos – Canadian Journal of Veterinary Research

Microbiome of death

From carrion to soil: microbial recycling of animal carcasses – Jennifer M. DeBruyn et al – Cell Trends in Microbiology

Water & extremophile microbiome

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient – Viviana Freire-Zapata et al – Nature Microbiology

Prescribed fire regimes influence responses of fungal and bacterial communities on new litter substrates in a brackish tidal marsh – Viet Q. Dao et al – PLOS One

Plant, root & soil microbiome

The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota – Anderson O. Oaikhena et al – Scientific Reports

Water‒soil-air‒plant mutual feedback mechanism under the application of red bed composite polymers – Tianpeng Chen et al – PLOS One

Diversity and community distribution of soil bacterial in the Yellow River irrigation area of Ningxia, China – Xia Wu et al – PLOS One

Bioinformatics & tools

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs – Annika Jochheim et al – BMC Microbiome