Category Archives: General Microbiome

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 8, 2024

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Get ready for #MVIF 33 & register here https://cassyni.com/s/mvif-33
See you next week!


Ecology and evolution

Community conservatism is widespread throughout microbial phyla and environments – Lukas Malfertheiner – bioRxiv 

Gut microbiome

Fecal microbiota transplantation alters the proteomic landscape of inflammation in HIV: identifying bacterial drivers – Claudio Díaz-García – Microbiome

Insights into the gut microbiome of vitiligo patients from India – Sudhir Kumar – BMC Microbiology

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

Pregnancy and Early Life Gut Microbiome: Influencing Factors and Health Implications – Trishla Sinha – Research Square

Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma in situ, and healthy women – Emma McCune – mSystems

Gut microbiota regulates stress responsivity via the circadian system – Gabriel S.S. Tofani – Cell Metabolism

Link to the post: https://twitter.com/gabriel_tofani/status/1853862878870446530

Oral microbiome

The role of the oral microbiota in the causal effect of adjunctive antibiotics on clinical outcomes in stage III–IV periodontitis patients – Sven Kleine Bardenhorst – Microbiome

Vaginal microbiome

Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study – Chloe Hicks – BJOG: An International Journal of Obstetrics and Gynaecology

Evaluation of the Vaginal Panel Realtime PCR kit (Vircell, SL) for diagnosing vaginitis: A comparative study with routinely used diagnostics – Isabel Amor – PlosOne

Animal experiments

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

Food microbiome

Review: Novel fermentations integrate traditional practice and rational design of fermented-food microbiomes – Dillon Arrigan – Current Biology

In-depth characterization of food and environmental microbiomes across different meat processing plants – Coral Barcenilla – Microbiome

Bioinformatics

Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases – Sriram Ramesh – PlosOne 

Techniques

DNA Extraction Protocols for Animal Fecal Material on Blood Spot Cards – Ann-Katrin Llarena – bioRxiv

Link to the post: https://twitter.com/svetlana_up/status/1854091197498683755
Link to the presentation: https://github.com/SvetlanaUP/presentations/blob/main/How_to_give_a_good_online_presentation_11_2024.pdf

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 18, 2024

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Human microbiome

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

Vaginal lactobacilli produce anti-inflammatory β-carboline compounds – Glick et al – Cell Host & Microbe

An ancient ecospecies of Helicobacter pylori  – Tourrette et al – Nature

Review – Intestinal fungal-host interactions in promoting and maintaining health – Hill & Round – Cell Host & Microbe

Review – Gut microbiome and health: mechanistic insights – de Vos et al – Gut

Animal microbiome

Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health – de Leon et al – Nature Microbiology

Stress triggers irritable bowel syndrome with diarrhea through a spermidine-mediated decline in type I interferon – Zhang et al – Cell Metabolism

Built environment

Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments  – Tong et al – Microbiome 

Plant microbiome

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations  – de Celis et al – Microbiome

Viruses

Using artificial intelligence to document the hidden RNA virosphere – Cell – Hou et al.

Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae – Rotman et al – Cell Host & Microbe

Bioinformatics

SurvBal: Compositional microbiome balances for survival outcomes – Li et al – Bioinformatics

q2-metnet: QIIME2 package to analyze 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota – Balzerani et al – Bioinformatics 

Non-microbiome

News feature – Your diet can change your immune system — here’s how – Nature

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 4, 2024

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Happy Friday! And see you next week at MVIF!

Plastisphere microbiome

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

Respiratory microbiome

Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis – Hongbin Chen – npj Biofilms and Microbiomes

Vaginal microbiome

Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples – Hayden N Brochu – bioRxiv

Oral microbiome

The intensive physical activity causes changes in the composition of gut and oral microbiota – Szymon Urban – Scientific Reports
⚽ “Twenty professional football players and twelve amateurs were invited to the study groups.”

Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome – Yuya Kiguchi – bioRxiv

The association between mode of childbirth delivery and early childhood caries: A comprehensive systematic review and meta-analysis – Li Xiang – PlosOne

Gut microbiome

What’s GABA got to do with it? A potential link between the microbiome, schizophrenia, and the endo-cannabinoid system – Ayala Glinert – Psychiatry Research

Changes in intestinal permeability and gut microbiota following diet-induced weight loss in patients with metabolic dysfunction-associated steatohepatitis and liver fibrosis – Dimitrios A. Koutoukidis – Gut Microbes

Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis – Yan Jia – Scientific Reports

Detailed Analysis of Prebiotic Fructo- and Galacto-Oligosaccharides in the Human Small Intestine – Mara P. H. van Trijp – Journal of Agricultural and Food Chemistry

Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape – Erica T. Grant – Microbiome

Human milk microbiome

Maternal HIV infection and the milk microbiome – Nicole H. Tobin – Microbiome

Viruses and phages

Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens – Mihály Koncz – Cell

Animals

Differential interactions of Rickettsia species with tick microbiota in Rh. sanguineus and Rh. turanicus – Apolline Maitre – Scientific Reports 

Animal experiments

Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer – Rachel C. Fellows – Science Advances

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

Plant, root, soil microbiome

Closing the gap: examining the impact of source habitat proximity on plant and soil microbial communities in post-mining spoil heap succession – Lenka Mészárošová – Frontiers in Microbiology

Bacterial Communities from the Antique Roman City of Carnuntum (Austria):16S r-RNA-Based Comparison of Soil Samples from Different Archaeological Horizons – Johann Michael Köhler – preprints

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

Phosphorus availability influences disease-suppressive soil microbiome through plant-microbe interactions – Yifan Cao – Microbiome

Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils – Luiz A. Domeignoz-Horta – Nature Communications

Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest – Madison Goforth – Plos One

Drinking water microbiome

Making waves: From tap to gut- exploring the impact of drinking water on gut microbiota – Hanieh Shakeri Moghaddam – Water Research

Bioinformatics

Taxometer: Improving taxonomic classification of metagenomics contigs – Svetlana Kutuzova – Nature Communications

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences – Yasas Wijesekara – bioRxiv

Emergent ecological patterns and modelling of gut microbiomes in health and in disease – Jacopo Pasqualini – Plos Computational Biology

Technique

Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing – Harry T. Child – Access Microbiology

Microbial community interactions on a chip – Duane S. Juang – PNAS