Tag Archives: microbiome

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 12, 2023

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Highlights!

A microbiota-modulated checkpoint directs immunosuppressive intestinal T cells into cancers – Marine Fidelle – Science 

Using gut microbiota as a diagnostic tool for colorectal cancer: machine learning techniques reveal promising results – Fang Lu – Journal of Medical Microbiology

Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes – Joshua B R White – Nature

Human and General Microbiome

Skin maturation from birth to 10 years of age: Structure, function, composition and microbiome – Georgios N Stamatas – Experimental Dermatology

Ecological principles of fecal microbiota transplantation – Francisco Dini-Andreote – Trends in Microbiology

Human Genetics Influences Microbiome Composition Involved in Asthma Exacerbations despite Inhaled Corticosteroid Treatment – Javier Perez-Garcia – The Journal of Allergy and Clinical Immunology

Gut bacterial metabolism contributes to host global purine homeostasis – Kazuyuki Kasahara – Cell Host & Microbe

The relative abundance of fecal bacterial species belonging to the Firmicutes and Bacteroidetes phyla is related to plasma levels of bile acids in young adults – Francisco J Osuna-Prieto – Metabolomics

The effect of vitamin D supplementation on the gut microbiome in older Australians – Results from analyses of the D-Health Trial – Hai Pham – Gut Microbes

Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage – Howell Leung – NPJ Biofilms and Microbiomes

Gut microbiota dysbiosis promotes the development of epithelial ovarian cancer via regulating Hedgehog signaling pathway – Xinyue Hu – Gut Microbes

Preprint: Microbes with higher metabolic independence are enriched in human gut microbiomes under stress – Iva Veseli – bioRxiv

Review: Evolutionary implications of host genetic control for engineering beneficial microbiomes – Lucas P Henry – Current Opinion in Systems Biology

Review: It’s all relative: analyzing microbiome compositions, its significance, pathogenesis and microbiota derived biofilms: Challenges and opportunities for disease intervention – Sahar Zaidi – Archives of Microbiology

Animal Microbiome

Gut microbiome helps honeybee (Apis mellifera) resist the stress of toxic nectar plant (Bidens pilosa) exposure: Evidence for survival and immunity – Qihe Tang – Environmental Microbiology

Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha) – Javad Sadeghi – Molecular Ecology

The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts – Jinlong Li – Environmental Microbiome

Association analysis of gut microbiota-metabolites-neuroendocrine changes in male rats acute exposure to simulated altitude of 5500 m – Jianan Wang – Scientific Reports

Microbiomes of Blood-Feeding Triatomines in the Context of Their Predatory Relatives and the Environment – Hassan Tarabai – Microbiology Spectrum

Beneficial Microbes and Compounds

Probiotic interventions promote metabolic health in high fat-fed hamsters in association with gut microbiota and endocannabinoidome alterations – S Lacroix – Beneficial Microbes

Strains of Faecalibacterium prausnitzii and its extracts reduce blood glucose levels, percent HbA1c, and improve glucose tolerance without causing hypoglycemic side effects in diabetic and prediabetic mice – John Kallassy – BMJ Open Diabetes Research & Care

Effects of a low FODMAP diet on gut microbiota in individuals with treated celiac disease having persistent gastrointestinal symptoms – a randomized controlled trial – Anne Mari Herfindal – The British Journal of Nutrition

Designed α-sheet peptides disrupt uropathogenic E. coli biofilms rendering bacteria susceptible to antibiotics and immune cells – Alissa Bleem – Scientific Reports

Review: ‘Multi-omics’ data integration: applications in probiotics studies – Iliya Dauda Kwoji – NPJ Science of Food

Review: Micro-/bio-/nano-/syn-encapsulations and co-treatments of bioactive microbial feed supplementation in augmenting finfish health and aquaculture nutrition: a review – P Puri – Beneficial Microbes

Plant Microbiome

Taxonomic analysis reveals host preference of rare fungi in endophytes of Vitis vinifera from the Czech Republic – Miroslav Kolařík – Folia Microbiologica

Environmental Microbiome

Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities – Samuel E Miller – mSystems

Built Environment

A new approach of microbiome monitoring in the built environment: feasibility analysis of condensation capture – Jarrad T Hampton-Marcell – Microbiome

Microbiome Research Tools and Techniques

Preprint: A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset – Cankun Wang – bioRxiv

Preprint: DeepBiomarker2: Prediction of alcohol and substance use disorder risk in post-traumatic stress disorder patients using electronic medical records and multiple social determinants of health – Oshin Miranda – Research Square

Latent Dirichlet Allocation modeling of environmental microbiomes – Anastasiia Kim – PLoS Computational Biology

When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities – Sandra Dedrick – mSystems

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 22, 2023

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Have a nice day. Today we have a long list!

Highlights!

Airway dysbiosis accelerates lung function decline in chronic obstructive pulmonary disease – Weijie Liang – Cell Host & Microbe

An integrated tumor, immune and microbiome atlas of colon cancer – Jessica Roelands – Nature Medicine

General and Human Microbiome 

Skin microbiome alterations in upper extremity secondary lymphedema – Adana-Christine Campbell – PloS One

Isolation and identification of hyaluronan-degrading bacteria from Japanese fecal microbiota – Hazuki Akazawa – PloS One

Bacterial and metabolic phenotypes associated with inadequate response to ursodeoxycholic acid treatment in primary biliary cholangitis – Laura Martinez-Gili – Gut Microbes

Gut microbiota and its relation to inflammation in patients with bipolar depression: a cross-sectional study – Tingting Huang – Annals of General Psychiatry

Alterations in the Gut Microbiome and Metabolisms in Pregnancies with Fetal Growth Restriction – Zixin Tao – Microbiology Spectrum

16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients – Maartje Kristensen – Microbiology Spectrum

Single-Molecule Approach to 16S rRNA for Vaginal Microbiome Signatures in Response to Metronidazole Treatment – Hanyu Qin – Microbiology Spectrum

The presence of intratumoral Porphyromonas gingivalis correlates with a previously defined pancreatic adenocarcinoma, immune cell expression phenotype and with tumor resident, adaptive immune receptor features – Jacob C Kinskey – Carcinogenesis

Commentary: Microbiome is the key to preventing anastomotic leak in colorectal surgery – James M Kinross – Gut

Commentary: The aerobiome-health axis: a paradigm shift in bioaerosol thinking – Jake M Robinson – Trends in Microbiology

Review: Impact of the host microbiota on fungal infections: new possibilities for intervention? – Eve W L Chow – Advanced Drug Delivery Reviews

Review: Malnourished Microbes: Host-Microbiome Interactions in Child Undernutrition – Helen J Jones – Annual Review of Nutrition

Review: A narrative review from gut to lungs: non-small cell lung cancer and the gastrointestinal microbiome – Hely Shah – Translational Lung Cancer Research

Review: The interplay between oral microbiota, gut microbiota and systematic diseases – Xiujun Tan – Journal of Oral Microbiology

Animal Model Microbiome

Exposing new taxonomic variation with inflammation – a murine model-specific genome database for gut microbiome researchers – Ikaia Leleiwi – Microbiome

Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic – Huan Li – BMC Microbiology

Alterations of the gut microbiome and metabolic profile in CVB3-induced mice acute viral myocarditis – Qing Kong – BMC Microbiology

Seaweed polysaccharides treatment alleviates injury of inflammatory responses and gut barrier in LPS-induced mice – Yuanyuan He – Microbial Pathogenesis

Non-model Animal Microbiome

An entomopathogenic fungus exploits its host humoral antibacterial immunity to minimize bacterial competition in the hemolymph – Jia-Lin Wang – Microbiome

Engineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees – Haoyu Lang – Nature Communications

New insights into microbial and metabolite signatures of coral bleaching – Hao Sun – The Science of the Total Environment

Feeding hempseed cake alters the bovine gut, respiratory and reproductive microbiota – Thomas M Winders – Scientific Reports

Composition of mucus- and digesta-associated bacteria in growing pigs with and without diarrhea differed according to the presence of colonic inflammation – Farhad M Panah – BMC Microbiology

The microbiome and gene expression of honey bee workers are affected by a diet containing pollen substitutes – J Elijah Powell – PloS One

Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens – Xiang-Yu Wang – BMC Microbiology

Built Environment

Diversity and compositional differences of the airborne microbiome in a biophilic indoor environment – Akinobu Toyoda – Scientific Reports

Plant Microbiome

Review: Engineering the Crop Microbiota Through Host Genetics – Carmen Escudero-Martinez – Annual Review of Phytopathology

Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.) – Angélica Jara-Servin – PloS One

Microbiome Analysis

News: Long-read sequencing for the metagenomic analysis of microbiomes – Tristan Free – BioTechniques

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

May 1, 2023

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Human and General Microbiome

Th17 cells sense microbiome to promote depressive-like behaviors – Eva M Medina-Rodriguez – Microbiome

Obese-associated gut microbes and derived phenolic metabolite as mediators of excessive motivation for food reward – Alice de Wouters d’Oplinter – Microbiome

Alteration of taste perception, food neophobia and oral microbiota composition in children with food allergy – Enza D’Auria – Scientific Reports

Translocating Lactobacillus torments tumors via tryptophan catabolism – Márcia S Pereira – Cell

Global trends in research related to the links between microbiota and antibiotics: a visualization study – Sa’ed H Zyoud – Scientific Reports

Modulation of antibiotic effects on microbial communities by resource competition – Daniel P Newton – Nature Communications

Review: Less is more: Antibiotics at the beginning of life – Martin Stocker – Nature Communications

Review: The interaction between autophagy, Helicobacter pylori, and gut microbiota in gastric carcinogenesis – Ali Nabavi-Rad – Trends in Microbiology

Review: The orchestra of human bacteriome by hormones – Arif Luqman – Microbial Pathogenesis

Review: Targeting the human gut microbiome with small-molecule inhibitors – Amelia Y M Woo – Nature Reviews. Chemistry

Review: A precision environmental health approach to prevention of human disease – Andrea Baccarelli – Nature Communications

Review: Emerging role of bacterial outer membrane vesicle in gastrointestinal tract – Cheng-Mei Tian – Gut Pathogens

Review: The Gut Microbiota – Brain Axis: Potential Mechanism of Drug Addiction – Xiao Luo – Current Topics in Medicinal Chemistry

Beneficial Microbes and Compounds

The effects of live and pasteurized Akkermansia muciniphila on DSS-induced ulcerative colitis, gut microbiota, and metabolomics in mice – Liangyu Xue – Food & Function

Inulin diet uncovers complex diet-microbiota-immune cell interactions remodeling the gut epithelium – Renan Oliveira Corrêa – Microbiome

Tumor-targeting engineered probiotic Escherichia coli Nissle 1917 inhibits colorectal tumorigenesis and modulates gut microbiota homeostasis in mice – Haibo Tang – Life Sciences

Animal Microbiome

Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition – Søren B Hansen – Genomics

Review: Environmental Effects on Bee Microbiota – Phuong N Nguyen – Microbial Ecology

Review: Illuminating the Oral Microbiome and its Host Interactions: Animal models of disease – George Hajishengallis – FEMS Microbiology Reviews

Plant Microbiome

Review: How does plant sex alter microbiota assembly in dioecious plants? – Qingxue Guo – Trends in Microbiology

Environmental Microbiome

Compositional Changes in Sediment Microbiota Are Associated with Seasonal Variation of the Water Column in High-Altitude Hyperarid Andean Lake Systems – Ignacio Ramos-Tapia – Microbiology Spectrum

Built Environment

Dynamics of microbial community composition during degradation of silks in burial environment – Bowen Wang – The Science of the Total Environment

Bioinformatics

DeepMicroGen: a generative adversarial network based method for longitudinal microbiome data imputation – Joung Min Choi – Bioinformatics

April 24, 2023

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Human and General Microbiome

Review: Effects of ultra-processed foods on the microbiota-gut-brain axis: The bread-and-butter issue – Zheyi Song – Food Research International 

Review: The emerging role of the small intestinal microbiota in human health and disease – Renate Ruigrok – Gut Microbes

Gut microbiome can predict chemoradiotherapy efficacy in patients with esophageal squamous cell carcinoma – Takuma Sasaki – Esophagus

Multi-omics signatures in new-onset diabetes predict metabolic response to dietary inulin: findings from an observational study followed by an interventional trial – N Ďásková – Nutrition & Diabetes

Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes – Kang Xiao – Journal of Microbiology

Sentinel or accomplice – gut microbiota and microglia cross-talk in disorders of gut-brain interaction – Haonan Zheng – Protein & Cell

Beneficial Microbes and Compounds

Effects of dietary fibers or probiotics on functional constipation symptoms and roles of gut microbiota: a double-blinded randomized placebo trial – Hao Lai – Gut Microbes

Review: Use of probiotic lactobacilli in the treatment of vaginal infections: In vitro and in vivo investigations – Peng Liu – Frontiers in Cellular and Infection Microbiology

Animal Microbiome

The hindgut microbiome contributes to host oxidative stress in postpartum dairy cows by affecting glutathione synthesis process – Fengfei Gu – Microbiome

Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons – Qi Li – NPJ Biofilms and Microbiomes

Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community – Manar El Samak – Marine Genomics

Vibrio cholerae Invasion Dynamics of the Chironomid Host Are Strongly Influenced by Aquatic Cell Density and Can Vary by Strain – Dianshu Zhao – Microbiology Spectrum

Antibiotic Conditioning Shapes Pseudosterile Mouse Models by Deleting Colonic Microbes Rather than Small Intestinal Microbes – Qingxue Chen – Microbiology Spectrum

Plant Microbiome

Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage – Zhiqiang Pang – Microbiome

Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions – Simrandeep Singh – Environmental Microbiome

Effects of vermicompost leachate on nitrogen, phosphorus, and microbiome in a food waste bioponic system – Sumeth Wongkiew – Journal of Environmental Management

The effect of wheat genotype on the microbiome is more evident in roots and varies through time – Liliana Quiza – ISME Communications

Environmental Microbiome

Disentangling temporal associations in marine microbial networks – Ina Maria Deutschmann – Microbiome

Evaluating the Reproducibility of Amplicon Sequencing Data Derived from Deep-Sea Cold Seep Sediment-Associated Microbiota – Jie Kong – Microbiology Spectrum

Built Environment

BioMateriOME: to understand microbe-material interactions within sustainable, living architectures – Beatriz Delgado Corrales – Advances in Applied Microbiology

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Deciphering associations between gut microbiota and clinical factors using microbial modules – Ran Wang – Bioinformatics

SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis – Jackie Zorz – ISME Communications

Integrating Multi-Omics Data to Construct Reliable Interconnected Models of Signaling, Gene Regulatory, and Metabolic Pathways – Krishna Kumar – Methods in Molecular Biology

Other

Interactions between the lipidome and genetic and environmental factors in autism – Chloe X Yap – Nature Medicine

April 17, 2023

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Human and General Microbiome

Large-scale phage cultivation for commensal human gut bacteria – Juntao Shen – Cell Host & Microbe

On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis – Felix M Key – Cell Host & Microbe

Staphylococcal diversity in atopic dermatitis from an individual to a global scale – Sara Saheb Kashaf – Cell Host & Microbe

A lncRNA from an inflammatory bowel disease risk locus maintains intestinal host-commensal homeostasis – Hongdi Ma – Cell Research

Coliphages of the human urinary microbiota – Elias Crum – PloS ONE

Children with autism show differences in the gut DNA virome compared to non-autistic children: a case control study – Aina Qu – BMC Pediatrics

Aerobic exercise training-induced alteration of gut microbiota composition affects endurance capacity – Masataka Uchida – The Journal of Physiology

Fusobacterium nucleatum aggravates rheumatoid arthritis through FadA-containing outer membrane vesicles – Mukeng Hong – Cell Host & Microbe

Review: Dental caries and their microbiomes in children: what do we do now? – Apoena Aguiar Ribeiro – Journal of Oral Microbiology

Review: Role of the Microbiome in Gut-Heart-Kidney Cross Talk – Griet Glorieux – Circulation Research

Review: Influence of Microbiota on Vaccine Effectiveness: Is the Microbiota the Key to Vaccine-induced Responses? – So-Hee Hong – Journal of Microbiology 

Review: Deciphering the quorum-sensing lexicon of the gut microbiota – Rita A Oliveira – Cell Host & Microbe

Review: The intratumoral microbiota: friend or foe? – Valentina Ferrari – Trends in Cancer

Review: Assembling symbiotic bacterial species into live therapeutic consortia that reconstitute microbiome functions – Rita A Oliveira – Cell Host & Microbe

Review: One population, multiple lifestyles: Commensalism and pathogenesis in the human mycobiome – Diana M Proctor – Cell Host & Microbe

Review: Cross-feeding in the gut microbiome: Ecology and mechanisms – Elizabeth J Culp – Cell Host & Microbe

Minireview: Networking between helminths, microbes, and mammals – P’ng Loke – Cell Host & Microbe

Commentary: The intratumoral microbiota: From microniches to single cells – Susan Bullman – Cell

Perspective: Designer bugs as cancer drugs? – Sairaj M Sajjath – Science

Animal Microbiome

Flagellar Genes Are Associated with the Colonization Persistence Phenotype of the Drosophila melanogaster Microbiota – Sarah J Morgan – Microbiology Spectrum

Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara – Konstantin Schmidt – eLife

Research Highlight: Urban bees reveal a city’s microbiome – Ashley York – Nature Reviews. Microbiology

Environmental Microbiome

Phyllosphere antibiotic resistome in a natural primary vegetation across a successional sequence after glacier retreat – Jian Li – Environment International

Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring – Shekhar Nagar – Applied Microbiology and Biotechnology