Tag Archives: bioinformatics

July 23, 2023

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Highlights!

Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome – Mohammad H Mirhakkak – Nature Communications

Depletion of butyrate-producing microbes of the Firmicutes predicts nonresponse to FMT therapy in patients with recurrent Clostridium difficile infection – Hongliang Tian – Gut Microbes

Chagas disease is related to structural changes of the gut microbiota in adults with chronic infection (TRIPOBIOME Study) – José A Pérez-Molina – PLoS Neglected Tropical Diseases

Human and General Microbiome

Study of the gut microbiome in Egyptian patients with Parkinson’s Disease – Mohammad Mehanna – BMC Microbiology

Intestinal microbiota controls graft-versus-host disease independent of donor-host genetic disparity – Motoko Koyama – Immunity

A systematic review exploring the association between the human gut microbiota and brain connectivity in health and disease – Danique Mulder – Molecular Psychiatry

A macroecological perspective on genetic diversity in the human gut microbiome – William R Shoemaker – PloS One

Gut microbiota metabolites mediate the interplay between childhood maltreatment and psychopathology in patients with eating disorders – Giovanni Castellini – Scientific Reports

In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract – Yeon Bee Kim – Scientific Reports

Host microbiome-pathogen interactions in pediatric infections – Jillian H Hurst – Current Opinion in Infectious Diseases

Intratumoural microbiome can predict the prognosis of hepatocellular carcinoma after surgery – Lejia Sun – Clinical and Translational Medicine

A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis – Brett A McGregor – Parasites & Vectors

Microbiome-derived cobalamin and succinyl-CoA as biomarkers for improved screening of anal cancer – Sergio Serrano-Villar – Nature Medicine

Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease – Gemma L D’Adamo – Cell Reports. Medicine

Multimodal immune cell phenotyping in GI biopsies reveals microbiome-related T cell modulations in human GvHD – Sebastian Jarosch – Cell Reports. Medicine

Beneficial Microbes and Compounds

Prebiotics and the risk of upper digestive tract and stomach cancers: the PrebiotiCa study – Federica Turati – Journal of the Academy of Nutrition and Dietetics

Plant Microbiome

Disturbance of eucalypt forests alters the composition, function, and assembly of soil microbial communities – Ernest D Osburn – FEMS Microbiology Ecology

Reciprocal influence of soil, phyllosphere, and aphid microbiomes – Adrian Wolfgang – Environmental Microbiome

Review: Co-evolution within the plant holobiont drives host performance – Fantin Mesny – EMBO Reports

Environmental Microbiome

May microbial ecological baseline exist in continental groundwater? – Sining Zhong – Microbiome

Evolutionary patterns of archaea predominant in acidic environment – Rafael Bargiela – Environmental Microbiome

Microbiome Research: Resources, Tools and Techniques

Machine learning-based approaches for cancer prediction using microbiome data – Pedro Freitas – Scientific Reports

Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products – Maria Victoria Fernandez-Cantos – Frontiers in Microbiology

A bioinformatic analysis of zinc transporters in intestinal Lactobacillaceae – Uyen Huynh – Metallomics

Uncovering the Carboxylated Metabolome in Gut Microbiota-Host Co-metabolism: A Chemical Derivatization-Molecular Networking Approach – Yan-Zhen Wang – Analytical Chemistry

July 16, 2023

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Human and General Microbiome

A two-sample mendelian randomization analysis investigates associations between gut microbiota and infertility – Taozhi Li – Scientific Reports

Targeting gut microbiota-derived kynurenine to predict and protect the remodeling of the pressure-overloaded young heart – Bozhong Shi – Science Advances

Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma – Hong Wu – Cancer Research

Metabolic and inflammatory profiles, gut microbiota and lifestyle factors in overweight and normal weight young thai adults – Surasawadee Somnuk – PloS One

Metagenomic assessment of gut microbial communities and risk of severe COVID-19 – Long H Nguyen – Genome Medicine

Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics – Arianna Basile – Gut Microbes

Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer – Sadaf Najafi – BMC Microbiology

Aerobic exercise training and gut microbiome-associated metabolic shifts in women with overweight: a multi-omic study – Jukka E Hintikka – Scientific Reports

Glycogen availability and pH variation in a medium simulating vaginal fluid influence the growth of vaginal Lactobacillus species and Gardnerella vaginalis – Stephany Navarro – BMC Microbiology

Antibiotic-induced gut microbiota dysbiosis has a functional impact on purine metabolism – Xin Liu – BMC Microbiology

Coarse graining the human gut microbiome – Christian Diener – Cell Host & Microbe

Review: Intestinal mucus and their glycans: A habitat for thriving microbiota – Ana S Luis – Cell host & Microbe

Review: https://www.cell.com/trends/immunology/fulltext/S1471-4906(23)00111-4 – Isabel Tarrant – Trends in Immunology

Review: A comprehensive perspective on the interaction between gut microbiota and COVID-19 vaccines – Ming Hong – Gut Microbes

Beneficial Microbes and Compounds

Bacillus coagulans MZY531 alleviates intestinal mucosal injury in immunosuppressive mice via modulating intestinal barrier, inflammatory response, and gut microbiota – Zhongwei Zhao – Scientific Reports

Microbiome Engineering Using Probiotic Yeast: Saccharomyces boulardii and the Secreted Human Lysozyme Lead to Changes in the Gut Microbiome and Metabolome of Mice – Jungyeon Kim – Microbiology Spectrum

Animal Microbiome

Neotropical bee microbiomes point to a fragmented social core and strong species-level effects – Jordan G Kueneman – Microbiome

Multi-Omics Reveals the Impact of Exogenous Short-Chain Fatty Acid Infusion on Rumen Homeostasis: Insights into Crosstalk between the Microbiome and the Epithelium in a Goat Model – Yongkang Zhen – Microbiology Spectrum

Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats – Huasong Bai – Microbiology Spectrum

First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome – J Eduardo Martinez-Hernandez – PeerJ

Plant Microbiome

The predictive power of phylogeny on growth rates in soil bacterial communities – Jeth Walkup – ISME Communications

Potential relevance between soybean nitrogen uptake and rhizosphere prokaryotic communities under waterlogging stress – Tengxiang Lian – ISME Communications

Effects of nitrogen reduction combined with bio-organic fertilizer on soil bacterial community diversity of red raspberry orchard – Xu Yuan – PloS One

Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome – Wenke Smets – mBio

Environmental Microbiome

Pathogen resistance in soils associated with bacteriome network reconstruction through reductive soil disinfestation – Weijing Zhu – Applied Microbiology and Biotechnology

Microbiome Research: Resources, Tools and Techniques

Detection of Microorganisms in Body Fluid Samples – Xin Ji – Methods in Molecular Biology 

Guidelines for Microbiome Studies in Renal Physiology – Rikeish R Muralitharan – American Journal of Physiology. Renal Physiology

Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions – Thiyagarajan Gnanasekaran – mSystems

Review: Activity-based protein profiling in microbes and the gut microbiome – Lin Han – Current Opinion in Chemical Biology

July 10, 2023

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Last week’s highlights

Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial – Bertrand Routy – Nature Medicine

Top-down identification of keystone taxa in the microbiome – Guy Amit – Nature Communications

Sources of gut microbiota variation in a large longitudinal Finnish infant cohort – Roosa Jokela – EBioMedicine

Events

11th Microbiome R&D and Business Collaboration Forum and 5th Probiotics & Prebiotics Congress: USA – San Diego, CA – October, 19 – 20, 2023

Human and General Microbiome

Essay: A microbiome exercise – Christoph A Thaiss – Science

Mendelian randomisation analysis reveals the possible causal relationship between infections, microbiota and clinical disease – Shifang Li – Gut

Microbiome variance of the small bowel in Crohn’s disease – Lucas Wauters – Gut

Metagenomics analysis of the neonatal intestinal resistome – Stefano Leo – Frontiers in Pediatrics

Development of the intestinal microbiome in cystic fibrosis in early life – Courtney E Price – mSphere

Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease – Yogesh Singh – Molecular Neurodegeneration

Male-Biased Gut Microbiome and Metabolites Aggravate Colorectal Cancer Development – Ling Wang – Advanced Science

Review: Systematic review: Autism spectrum disorder and the gut microbiota – Jenni Korteniemi – Acta Psychiatrica Scandinavica

Review: Early-life respiratory infections and developmental immunity determine lifelong lung health – Clare M Lloyd – Nature Immunology

Microbiome and Evolution

Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life – Mia M Keady – PNAS

Shared evolutionary path in social microbiomes – Nelson Frazão – Molecular Biology and Evolution

Beneficial Microbes and Compounds

Review: Use of probiotics, prebiotics, and synbiotics in non-alcoholic fatty liver disease: A systematic review and meta-analysis – Lim Rong – Journal of Gastroenterology and Hepatology

Akkermansia muciniphila and Bifidobacterium bifidum Prevent NAFLD by Regulating FXR Expression and Gut Microbiota – Fulin Nian – Journal of Clinical and Translational Hepatology

Limosilactobacillus reuteri inhibits the acid tolerance response in oral bacteria – Gabriella Boisen – Biofilm

Animal Microbiome

Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome – Aravindh Nagarajan – Microbiome

Selection for environmental variance shifted the gut microbiome composition driving animal resilience – Cristina Casto-Rebollo – Microbiome

Plant Microbiome

Metabolic interaction models recapitulate leaf microbiota ecology – Martin Schäfer – Science

Environmental Microbiome

Microeukaryotic predators shape the wastewater microbiome – Nils Heck – Water Research

Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples – Cátia Santos-Pereira – Applied Microbiology and Biotechnology

Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes – Jeanett Daga-Quisbert – FEMS Microbiology Ecology

Built Environment

Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea – E Anders Kiledal – Microbiology Spectrum

Microbiome Research: Resources, Tools and Techniques

A catalog of bacterial reference genomes from cultivated human oral bacteria – Wenxi Li – NPJ Biofilms and Microbiomes

Gene-based microbiome representation enhances host phenotype classification – Thomas Deschênes – mSystems

Integrative meta-omics in Galaxy and beyond – Valerie C Schiml – Environmental Microbiome

Preprint: Compositional analysis of microbiome data using the linear decomposition model (LDM) – Yi-Juan Hu – bioRxiv

Preprint: Processing and Storage Methods Affect Oral and Gut Microbiome Composition – Dorothy K Superdock – bioRxiv

Preprint: A genome catalog of the early-life human skin microbiome – Zeyang Shen – bioRxiv

Review: In vitro models as a tool to study the role of gut microbiota in obesity – Abigail González – Critical Reviews in Food Science and Nutrition

July 3, 2023

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Human and General Microbiome

Bacterial Community Modifies Host Genetics Effect on Early Childhood Caries – F Blostein – Journal of Dental Research

Clostridioides difficile infection in infants: a case report and literature review – Zhirong Li – Gut Pathogens

The microbiota of pregnant women with SARS-CoV-2 and their infants – Heidi K Leftwich – Microbiome

Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles – James T Morton – Nature Neuroscience

Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet- and host-derived glycans – Mariana G Sartorio – PNAS

Site-specialization of human oral Gemella species – Julian Torres-Morales – Journal of oral Microbiology

Review: Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy – Andrew Maltez Thomas – Nature Reviews. Clinical Oncology

Review: Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics – Teija Ojala – Trends in Genetics

Review: Bacteria from the gut influence the host micronutrient status – Dorgeles Kouakou Dje Kouadio – Critical Reviews in Food Science and Nutrition

Beneficial Microbes and Compounds

Milk kefir alters fecal microbiota impacting gut and brain health in mice – Mariana de Fátima Albuquerque Pereira – Applied Microbiology and Biotechnology

Review: Calorie restriction mimetic drugs could favorably influence gut microbiota leading to lifespan extension – Tomoya Shintani – GeroScience

Are probiotics, prebiotics, and synbiotics beneficial in primary thyroid diseases? A systematic review with meta-analysis – Karolina Zawadzka – Annals of Agricultural and Environmental Medicine

Akkermansia muciniphila and Lactobacillus plantarum ameliorate systemic lupus erythematosus by possibly regulating immune response and remodeling gut microbiota – Mengchen Guo – mSphere

Effect of prebiotics, probiotics, synbiotics on depression: results from a meta-analysis – Qin Zhang – BMC Psychiatry

Animal Microbiome and Animal Model Microbiome

Patterns and determinants of the global herbivorous mycobiome – Casey H Meili – Nature Communications

Resistant starches from dietary pulses modulate the gut metabolome in association with microbiome in a humanized murine model of ageing – Saurabh Kadyan – Scientific Reports

The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats – Hanna Angstmann – Environmental Microbiome

Plant Microbiome

Different Techniques reveal the Difference of Community Structure and Function of Fungi from Root and Rhizosphere of Salvia miltiorrhiza Bunge – C Li – Plant Biology (Stuttgart, Germany)

Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth – Beatriz Lagunas – Microbiome

Core community drives phyllosphere bacterial diversity and function in multiple ecosystems – Ran Xue – The Science of the Total Environment

Environmental Microbiome

A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment – David Madrigal-Trejo – Microbial Ecology

Microbiome Research: Resources, Tools and Techniques

MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities – Billy Taj – Microbiome

Supervised learning and model analysis with compositional data – Shimeng Huang – PLoS Computational Biology

Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities – Qi Wang – Bioinformatics

Creation of a milk oligosaccharide database, MilkOligoDB, reveals common structural motifs and extensive diversity across mammals – Sierra D Durham – Scientific Reports

Review: Genetic Engineering of Resident Bacteria in the Gut Microbiome – Jack Arnold – Journal of Bacteriology

Review: Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA – Lin Yang – Nature Protocols

June 26, 2023

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Highlights!

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes – Matthew M Carter – Cell

A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression – Lauren E Davey – Nature Microbiology

The first international Rome consensus conference on gut microbiota and faecal microbiota transplantation in inflammatory bowel disease – Loris Riccardo Lopetuso – Gut

Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors – Julien Tap – Nature Communications

Human and General Microbiome

Key bacterial taxa determine longitudinal dynamics of aromatic amino acid catabolism in infants’ gut – Martin F Laursen – Gut Microbes

Low diversity microbiota and an increased metabolism of arginine and aromatic amino acids: a hallmark of hepatic encephalopathy in western Mexican patients with alcohol-associated cirrhosis – Tonatiuh Abimael Baltazar-Díaz – Journal of Applied Microbiology

Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy – Gang Fan – Gut Microbes

Species-Specific Analysis of Bacterial Vaginosis-Associated Bacteria – John Osei Sekyere – Microbiology Spectrum

Gut microbiota in nonalcoholic fatty liver disease: a PREDIMED-Plus trial sub analysis – Ana María Gómez-Pérez – Gut Microbes

Associations of Circulating Estrogens and Estrogen Metabolites with Fecal and Oral Microbiome in Postmenopausal Women in the Ghana Breast Health Study – Zeni Wu – Microbiology Spectrum

Meta-analysis of the effects of proton pump inhibitors on the human gut microbiota – Jiayi Zhang – BMC Microbiology

Animal Microbiome

Gut microbiomes of captive primates show phylosymbiosis, respond to dietary sugar reduction, and select for host-specific dietary microbes – Sally L Bornbusch – FEMS Microbiology Ecology

Environmental Microbiome

Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome – Xiaolan Lin – Microbiome

Microbiome Research: Resources, Tools and Techniques

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation – Dileep Kishore – mSystems

Human microbiome cultivation expands with AI – Marta Selma-Royo – Nature Biotechnology

GutBug: A Tool for Prediction of Human Gut Bacteria Mediated Biotransformation of Biotic and Xenobiotic Molecules Using Machine Learning – Aditya S Malwe – Journal of Molecular Biology

Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome – Céline Elie – Scientific Reports

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome – Elliot M Lee – mSystems

Assumptions on decision making and environment can yield multiple steady states in microbial community models – Axel Theorell – BMC Bioinformatics

EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies – Mayar Shahin – NPJ Systems Biology and Applications

Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy – Oshrit Shtossel – Gut Microbes

June 19, 2023

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Highlights!

A data-driven approach for predicting the impact of drugs on the human microbiome – Yadid M Algavi – Nature Communications

CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection – Lingdi Zhang – Microbiome

Human and General Microbiome

Gut and oral microbiome modulate molecular and clinical markers of schizophrenia-related symptoms: A transdiagnostic, multilevel pilot study – Jakleen J Lee – Psychiatry Research

Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: A blinded randomized controlled trial – Lepeng Zhou – Cell Host & Microbe

Metaproteomics Characterizes the Human Gingival Crevicular Fluid Microbiome Function in Periodontitis – Xiaolian Xiao – Journal of Proteome Research

Generation of dysbiotic microbiota in cutaneous leishmaniasis and enhancement of skin inflammation – Shumaila Naz – Microbial Pathogenesis

Oral microbiota may affect osteoradionecrosis following radiotherapy for head and neck cancer – Zhengrui Li – Journal of Translational Medicine

Oral microbial communities in 5-year-old children with versus without dental caries – Zhengyan Yang – BMC Oral Health

Analysis of gut microbiota in patients with Williams-Beuren Syndrome reveals dysbiosis linked to clinical manifestations – Federica Del Chierico – Scientific Reports

Review: Aspects of oral streptococcal metabolic diversity: Imagining the landscape beneath the fog – Peter Zuber – Molecular Microbiology

Review: Challenges and strategies for preventing intestinal damage associated to mercury dietary exposure – Pilar Rodríguez-Viso – Toxicology

Animal Microbiome

Phylogenetic comparative approach reveals evolutionary conservatism, ancestral composition, and integration of vertebrate gut microbiota – Benoît Perez-Lamarque – Molecular Biology and Evolution

Social transmission of bacterial symbionts homogenizes the microbiome within and across generations of group-living spiders – Clémence Rose – ISME Communications

Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation – Alexandra D Switzer – Environmental Microbiology

Microbiome Research Tools and Techniques

The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia – Jonas Schluter – Cell Host & Microbe

MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets – Matthys G Potgieter – PLoS Computational Biology

Methods for Analyzing the Gut Microbiota in Diabetic Retinopathy – Yinhua Huang – Methods in Molecular Biology

Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution – Atsufumi Ohta – Scientific Reports

June 5, 2023

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Human and General Microbiome

Altered gut microbiota as potential biomarker biomarkers for autism spectrum disorder in early childhood – Yingxin Zhao – Neuroscience

The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination – M Laura Rolon – Microbiome

Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort – Shantelle Claassen-Weitz – Microbiome

Secreted Akkermansia muciniphila threonyl-tRNA synthetase functions to monitor and modulate immune homeostasis – Su-Man Kim – Cell Host & Microbe

Gut Microbiome Composition is associated with future onset of Crohn’s Disease in Healthy First-Degree Relatives – Juan Antonio Raygoza Garay – Gastroenterology

Metagenome Investigation of Ocular Microbiota of Cataract Patients With and Without Type 2 Diabetes – Zheng Shao – Translational Vision Science & Technology

Longitudinal Gut Microbiota Dysbiosis Underlies Olanzapine-Induced Weight Gain – Li Qian – Microbiology Spectrum

Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut – Ida Ormaasen – BMC Genomics

Review: The Microbiome in Advanced Melanoma: Where Are We Now? – Dylan D Fortman – Current Oncology Reports

Review: Human gut microbiome: A primer for the clinician – Saurabh Kedia – JGH Open

Review: Role of gut microbiota and bacterial metabolites in mucins of colorectal cancer – Ming Gu – Frontiers in Cellular and Infection Microbiology

Beneficial Microbes and Compounds

Bacteriophage targeting microbiota alleviates non-alcoholic fatty liver disease induced by high alcohol-producing Klebsiella pneumoniae – Lin Gan – Nature Communications

Clostridium butyricum improves cognitive dysfunction in ICV-STZ-induced Alzheimer’s disease mice via suppressing TLR4 signaling pathway through the gut-brain axis – Yunfang Su – PloS One

Review: Regulation of gut microbiota by vitamin C, vitamin E and β-carotene – Xin-Yu Li – Food Research International

Animal Microbiome

Diversity of the Pacific Ocean coral reef microbiome – Pierre E Galand – Nature Communications

Effects of Aeromonas hydrophila infection on the intestinal microbiota, transcriptome, and metabolomic of common carp (Cyprinus carpio) – Lan Zhang – Fish & Shellfish Immunology

Genital tract microbiome dynamics are associated with time of Chlamydia infection in mice – Lihong Zhao – Scientific Reports

Environmental Microbiome

The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival – Benjamin J Wainwright – Environmental Microbiome

Microbiome Research Tools and Techniques

Formation and Analysis of Mono-species and Polymicrobial Oral Biofilms in Flow-Cell Models – Jessica Neilands – Methods in Molecular Biology

MAIRA: Protein-based Analysis of MinION Reads on a Laptop – Caner Bağcı – Methods in Molecular Biology 

Recovery and Analysis of Long-Read Metagenome-Assembled Genomes – Krithika Arumugam – Methods in Molecular Biology 

Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding – Marie-Pierre Chapuis – Molecular Ecology Resources

May 29, 2023

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Highlights!

Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains – Raymond Kiu – Nature Microbiology

Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach – Conor Feehily – Nature Communications

Human and General Microbiome

Expanding the repertoire of counterselection markers for markerless gene deletion in the human gut bacterium Phocaeicola vulgatus – André Neff – Anaerobe

Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection – Zheng Wang – Microbiome

Symbiotic microbiome Staphylococcus epidermidis restricts IL-33 production in allergic nasal epithelium via limiting the cellular necroptosis – Yung Jin Jeon – BMC Microbiology

Gut microbiome associated with low anterior resection syndrome after rectal cancer surgery – Min Jung Kim – Scientific Reports

Metabolomics Reveals Gut Microbiota Contribute to PPARα Deficiency-Induced Alcoholic Liver Injury – Ting Zhang – Journal of Proteome Research

Following your gut: the emerging role of the gut microbiota in predicting and treating immune-related adverse events – Antoine Desilets – Current Opinion in Oncology

Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma – Spyridon Megremis – Scientific Reports

The causal links between gut microbiota and COVID-19: A Mendelian randomization study – Jukun Song – Journal of Medical Virology

The Sexome – A proof of concept study into microbial transfer between heterosexual couples after sexual intercourse – Ruby Dixon – Forensic Science International

A systematic review of the protein composition of whole saliva in subjects with healthy periodontium compared with chronic periodontitis – Ana G Sánchez-Medrano – PloS ONE

Microbiome, Food and Diet

Metagenomic analysis and antibacterial activity of kefir microorganisms – Brianda D González-Orozco – Journal of Food Science

Fecal Metabolites as Biomarkers for Predicting Food Intake by Healthy Adults – Leila M Shinn – The Journal of Nutrition

More Microbes

Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota – Afaf Hamame – Scientific Reports

Animal Microbiome

Gut microbiome signatures of extreme environment adaption in Tibetan pig – Fangfang Zhao – NPJ Biofilms and Microbiomes

Holobiont Evolution: Population Theory for the Hologenome – Joan Roughgarden – The American Naturalist

Plant Microbiome

Integration of Phenotypes in Microbiome Networks for Designing Synthetic Communities: a Study of Mycobiomes in the Grafted Tomato System – Ravin Poudel – Applied and Environmental Microbiology

Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum – Jilu Che – Microbiology Spectrum

Bioinformatics, Microbiome Analysis and Techniques

MDM-Pred: a freely available web application for predicting the metabolism of drug-like compounds by the gut microbiota – A S Kolodnitsky – SAR and QSAR in Environmental Research

HONMF: integration analysis of multi-omics microbiome data via matrix factorization and hypergraph – Yuanyuan Ma – Bioinformatics 

Bayesian compositional regression with microbiome features via variational inference – Darren A V Scott – BMC Bioinformatics

The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae – Katherine M Elston – ISME Communications

Review: Unravelling animal-microbiota evolution on a chip – Ostaizka Aizpurua – Trends in Microbiology

May 15, 2023

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Human Microbiome

Assessing the relationship between gut microbiota and irritable bowel syndrome: a two-sample Mendelian randomization analysis – Bin Liu – BMC Gastroenterology

The oral microbiota is a reservoir for antimicrobial resistance: resistome and phenotypic resistance characteristics of oral biofilm in health, caries, and periodontitis – A C Anderson – Annals of Clinical Microbiology and Antimicrobials

New evidence for the role of gut microbiota on atrial fibrillation development – Christopher Papandreou – EBioMedicine

Influence of grape consumption on the human microbiome – Asim Dave – Scientific Reports

Microbiota transplant to control inflammation in a patient with NLRC4 gain-of-function-induced disease – Claudia Bracaglia – The Journal of Allergy and Clinical Immunology

Review: Ecology of the respiratory tract microbiome – Ana Elena Pérez-Cobas – Trends in Microbiology

Animal Microbiome

Integrated microbiome-metabolome-genome axis data of Laiwu and Lulai pigs – Xueshuang Lai – Scientific data

Positive associations matter: Microbial relationships drive tick microbiome composition – Nicholas M Fountain-Jones – Molecular Ecology

In Vitro Ileal Fermentation is Affected More by the Fiber Source Fermented than the Ileal Microbial Composition in Growing Pigs – Anna Me Hoogeveen – Current Developments in Nutrition

Oroxin B improves metabolic-associated fatty liver disease by alleviating gut microbiota dysbiosis in a high-fat diet-induced rat model – Yuhong Huang – European Journal of Pharmacology

Plant Microbiome

Drought stress mediated differences in phyllosphere microbiome and associated pathogen resistance between male and female poplars – Tiantian Lin – The Plant Journal 

Environmental Microbiome

Looking into sewage: how far can metagenomics help to detect human enteric viruses? – Julien Schaeffer – Frontiers in Microbiology

Metagenomic insights into the potential risks of representative bio/non-degradable plastic and non-plastic debris in the upper and lower reaches of Haihe Estuary, China – Xinhai Zhao – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

A Bayesian joint model for compositional mediation effect selection in microbiome data – Jingyan Fu – Statistics in Medicine

May 8, 2023

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General and Human Microbiome

Microbial β-glucuronidases drive human periodontal disease etiology – Adam D Lietzan – Science Advances

Vaginal epithelial dysfunction is mediated by the microbiome, metabolome, and mTOR signaling – Alicia R Berard – Cell Reports

Causal relationship between Gut Microbiota and Obstructive sleep apnea – Yi Wei – Archives of Gerontology and Geriatrics

Changes in the intestinal microbiota of children with hand, foot, and mouth disease under 3 years old – Su Yue Zhu – Medicine

Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection – Cinthya Ruiz-Tagle – Scientific Reports

Pitfalls in sampling and analyzing low-biomass human nasal microbiome samples – Petra Pjevac – The Journal of Allergy and Clinical Immunology

The saga of non-traditional risk factors continues with proteomics, microbiome, ozone, ketone bodies, and depression: let us rethink prevention – Filippo Crea – European Heart Journal

Review: Stress, inflammation, microbiome and depression – Eva M Medina-Rodriguez – Pharmacology, Biochemistry, and Behavior

Review: Fungi and cancer – Aurelia Saftien – Gut

Review: L-Fucose is involved in human-gut microbiome interactions – Jungyeon Kim – Applied Microbiology and Biotechnology

Beneficial Microbes, Compounds and Interventions

Vitamin K2 supplementation improves impaired glycemic homeostasis and insulin sensitivity for type 2 diabetes through gut microbiome and fecal metabolites – Yuntao Zhang – BMC Medicine

Intermittent fasting alleviates non-alcoholic steatohepatitis by regulating bile acid metabolism and promoting fecal bile acid excretion in high-fat and high-cholesterol diet fed mice – Xiaozhuan Lin – Molecular Nutrition & Food Research

Animal Microbiome

Gut microbiome of mealworms (Tenebrio molitor Larvae) show similar responses to polystyrene and corn straw diets – Tursunay Mamtimin – Microbiome

Plant Microbiome

Review: The good, the bad, and the phosphate: regulation of beneficial and detrimental plant-microbe interactions by the plant phosphate status – Michael Paries – The New Phytologist