Tag Archives: animal models

May 15, 2023

Posted on by

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

Posted on by

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

Posted on by

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

Posted on by

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

Posted on by

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

April 10, 2023

Posted on by

Human and General Microbiome

Review: Exploring the Influence of Gut Microbiome on Energy Metabolism in Humans – Julia Montenegro – Advances in Nutrition

Review: Ruminococcus gnavus: friend or foe for human health – Emmanuelle H Crost – FEMS Microbiology Reviews

Uncovering the special microbiota associated with occurrence and progression of gastric cancer by using RNA-sequencing – Bin Ai – Scientific Reports

Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism – Xiangwei Hu – NPJ Biofilms and Microbiomes

The secondary bile acid isoursodeoxycholate correlates with post-prandial lipemia, inflammation, and appetite and changes post-bariatric surgery – Panayiotis Louca – Cell Reports. Medicine

Forging the microbiome to help us live long and prosper – Rachel R Rock – PLoS Biology

Meta-analysis reveals Helicobacter pylori mutual exclusivity and reproducible gastric microbiome alterations during gastric carcinoma progression – Yan Li – Gut Microbes

Beneficial Microbes and Compounds

Lacticaseibacillus rhamnosus Probio-M9 enhanced the antitumor response to anti-PD-1 therapy by modulating intestinal metabolites – Guangqi Gao – EBioMedicine

Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems – Samuel Zimmerman – mSystems

New carbohydrate binding domains identified by phage display based functional metagenomic screens of human gut microbiota – Akil Akhtar – Communications Biology

Animal Microbiome

Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community – Jacob Agerbo Rasmussen – Microbiological Research

Plant Microbiome

Cofunctioning of bacterial exometabolites drives root microbiota establishment – Felix Getzke – PNAS

Environmental Microbiome

Review: Unveiling the role of emerging metagenomics for the examination of hypersaline environments – Kiran Dindhoria – Biotechnology & Genetic Engineering Reviews

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Multi-scale Adaptive Differential Abundance Analysis in Microbial Compositional Data – Shulei Wang – Bioinformatics

The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection – Ruijie Xu – PloS ONE

An in vitro platform for study of the human gut microbiome under an oxygen gradient – James Comolli – Biomedical Microdevices

Machine learning model to predict obesity using gut metabolite and brain microstructure data – Vadim Osadchiy – Scientific Reports

April 3, 2023

Posted on by

Human and General Microbiome

Review: Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome – Stephen R Stockdale – Current Opinion in Microbiology

No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C S Tan – Nature Microbiology

Genetic correlations between Alzheimer’s disease and gut microbiome genera – Davis Cammann – Scientific Reports

Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma – Christopher Delaney – APMIS

Mendelian randomization analyses reveal causal relationships between the human microbiome and longevity – Xiaomin Liu – Scientific Reports

Genomics of Invasive Cutibacterium acnes Isolates from Deep-Seated Infections – Anna Both – Microbiology Spectrum

Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition – Kayla A Carter – mSystems

Review: Interspecies Interactions within the Host: the Social Network of Group B Streptococcus – Marlyd E Mejia – Infection and Immunity

Beneficial Microbes and Compounds

Review: Kefir as a therapeutic agent in clinical research: a scoping review – Milena Klippel Bessa – Nutrition Research Reviews

Interaction between β-glucans and gut microbiota: a comprehensive review – Reza Karimi – Critical Reviews in Food Science and Nutrition

Combination of vitamin D and probiotics inhibits chemically induced colorectal carcinogenesis in Wistar rats – Carolina S de Oliveira – Life Sciences

Animal Microbiome

Review: Recent advancements in coral health, microbiome interactions and climate change – Nizam Ashraf – The Science of the Total Environment

Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome – Line Jensen Ostenfeld – PloS One

Microbial Species-Area Relationships on the Skins of Amphibian Hosts – Fan Yang – Microbiology Spectrum

Intestinal microbiota of Nearctic-Neotropical migratory birds vary more over seasons and years than between host species – Heather R Skeen – Molecular Ecology

Food Microbiome

A unique case in which Kimoto-style fermentation was completed with Leuconostoc as the dominant genus without transitioning to Lactobacillus – Kohei Ito – Journal of Bioscience and Bioengineering

Built Environment

Holobiont Urbanism: sampling urban beehives reveals cities’ metagenomes – Elizabeth Hénaff – Environmental Microbiome

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Contamination detection and microbiome exploration with GRIMER – Vitor C Piro – GigaScience

Annotation-free discovery of functional groups in microbial communities – Xiaoyu Shan – Nature Ecology & Evolution

ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis – Jinlong Ru – Gut Microbes

Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition – Line Roager – Microbiology Spectrum

Preprint: Identifying keystone species in microbial communities using deep learning – Xu-Wen Wang – bioRxiv

March 27, 2023

Posted on by

Human and General Microbiome

The genomic landscape of reference genomes of cultivated human gut bacteria – Xiaoqian Lin – Nature Communications

Inhibition of a Microbiota-derived Peptide Ameliorates Established Acute Lung Injury – Valeria Fridman D’Alessandro – The American Journal of Pathology

Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study – Vladimir Ivashkin – BMC Gastroenterology

Mucin glycans drive oral microbial community composition and function – Chloe M Wu – NPJ Biofilms and Microbiomes

Changes in gut microbial community upon chronic kidney disease – Wu Liu – PloS One

A Pilot Study Exploring Temporal Development of Gut Microbiome/Metabolome in Breastfed Neonates during the First Week of Life – Imad Awan – Pediatric Gastroenterology, Hepatology & Nutrition

Realising respiratory microbiomic meta-analyses: time for a standardised framework – David Broderick – Microbiome

Vulvovaginal yeast infections during pregnancy and perinatal outcomes: systematic review and meta-analysis – Ranjana M S Gigi – BMC Women’s Health

Preprint: Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice – Rebecca H Gellman – bioRxiv

Review: Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules – Eileen Ryan – Microbiology

Review: Impact of Intermittent Fasting on the Gut Microbiota: A Systematic Review – Theodoro Pérez-Gerdel – Advanced Biology

Animal Microbiome

Wolbachia endosymbiotic bacteria alter the gut microbiome in the fly Drosophila nigrosparsa – Matsapume Detcharoen – Journal of Invertebrate Pathology

A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota – Ren Dodge – Nature Communications

Plant Microbiome

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species – Sarah McLaughlin – Nature Communications

Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria – Martina Cardoni – Environmental Microbiome

Environmental Microbiome

Investigating the eco-evolutionary response of microbiomes to environmental change – Jennifer B H Martiny – Ecology Letters

Microbiome Analysis: Resources, Tools and Techniques

In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea – Alba Regueira-Iglesias – Microbiome

DeepGeni: deep generalized interpretable autoencoder elucidates gut microbiota for better cancer immunotherapy – Min Oh – Scientific Reports

Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes – Mingqian Zhang – Bioinformatics

Preprint: Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research – Jonathan L Golob – medRxiv

March 20, 2023

Posted on by

Human and General Microbiome

Bacteria require phase separation for fitness in the mammalian gut – Emilia Krypotou – Science

Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets – Jonathan J Panzer – BMC Microbiology

Gut-microbiome-expressed 3β-hydroxysteroid dehydrogenase degrades estradiol and is linked to depression in premenopausal females – Di Li – Cell Metabolism

Metagenomic association analysis of cognitive impairment in community-dwelling older adults – Jincheng Li – Neurobiology of Disease

Fusobacterium nucleatum promotes esophageal cancer early occurrence through upregulation of IL-32/PRTN3 expression – Jing Lei – Cancer Science

Review: Postbiotics Implication in the Microbiota-Host Intestinal Epithelial Cells Mutualism – Harpreet Kaur – Probiotics and Antimicrobial Proteins

Review: Microbiota and growth among infants and children in low-income and middle-income settings – James M Njunge – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective – Mireia Valles-Colomer – Nature Medicine

Review: Oral polymicrobial communities: Assembly, function, and impact on diseases – George Hajishengallis – Cell Host & Microbe

Review: Gut microbiota: a non-target victim of pesticide-induced toxicity – Tusha Sharma – Gut Microbes

Perspective: Human microbiome research: Growing pains and future promises – Jens Puschhof – PLoS Biology

Beneficial Microbes and Compounds

Versatility of bacterial outer membrane vesicles in regulating intestinal homeostasis – Xinyue Wang – Science Advances

Lactobacillus rhamnosus GG cell-free supernatant as a novel anti-cancer adjuvant – Rossella Salemi – Journal of Translational Medicine

Environmental Microbiome

Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy – Eke I Kalu – ISME Communications

Other Microbes

Biointerface mineralization generates ultraresistant gut microbes as oral biotherapeutics – Zhongmin Geng – Science Advances

Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli – Tracy H Hazen – Nature Communications

Microbiome Analysis: Tools and Techniques

Spatial profiling of microbial communities by sequential FISH with error-robust encoding – Zhaohui Cao – Nature Communications

sBGC-hm: An atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome – Huixi Zou – Bioinformatics

Protocol: Bioinformatic and Statistical Analysis of Microbiome Data – Youngchul Kim – Methods in Molecular Biology

Protocol: Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications – Xuefeng Wang – Methods in Molecular Biology

March 13, 2023

Posted on by

Human and General Microbiome

Dysbiosis of a microbiota-immune metasystem in critical illness is associated with nosocomial infections – Jared Schlechte – Nature Medicine

Altered infective competence of the human gut microbiome in COVID-19 – Laura de Nies – Microbiome

Impact of high altitude on composition and functional profiling of oral microbiome in Indian male population – Manisha Kumari – Scientific Reports

Incidence of Breast Cancer and Enterococcus Infection: A Retrospective Analysis – Matthew Cardeiro – World Journal of Oncology

Multi-omics studies in interpreting the evolving standard model for immune functions – Dipyaman Ganguly – Briefings in Functional Genomics

Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans – Jinuk Jeong – Journal of oral Microbiology

A transcriptomic insight into the human sperm microbiome through next-generation sequencing – Celia Corral-Vazquez – Systems Biology in Reproductive Medicine

Beneficial Microbes and Compounds

Metformin alleviates liver fibrosis in mice by enriching Lactobacillus sp. MF-1 in the gut microbiota – Tao Yang – Biochimica et Biophysica Acta

Animal Microbiome

Microbiota alters the metabolome in an age- and sex- dependent manner in mice – Kirsty Brown – Nature Communications

IL-22 alters gut microbiota composition and function to increase aryl hydrocarbon receptor activity in mice and humans – Jordan S Mar – Microbiome

Decreased Paneth cell α-defensins promote fibrosis in a choline-deficient L-amino acid-defined high-fat diet-induced mouse model of nonalcoholic steatohepatitis via disrupting intestinal microbiota – Shunta Nakamura – Scientific Reports

Plant Microbiome

Microbiota and functional analyses of nitrogen-fixing bacteria in root-knot nematode parasitism of plants – Ye Li – Microbiome

Non-volatile metabolites mediating plant interactions with insect herbivores – Mei Luo – The Plant Journal

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress – Bo Wang – Frontiers in Microbiology

Review: Emerging Pathways for Engineering the Rhizosphere Microbiome for Optimal Plant Health – Shengdie Yang – Journal of Agricultural and food Chemistry

Microbiome Analysis: Tools and Techniques

A bayesian zero-inflated dirichlet-multinomial regression model for multivariate compositional count data – Matthew D Koslovsky – Biometrics

Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples – Ruben López-Aladid – Scientific Reports