Tag Archives: Microbiome Digest

December 29, 2023

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Human and General Microbiome

Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults – Xuanji Li – Nature Communications

Social anxiety disorder-associated gut microbiota increases social fear – Nathaniel L Ritz – PNAS

Plasmid-encoded toxin defence mediates mutualistic microbial interactions – Sarah Moraïs – Nature Microbiology

Oral microbiome-driven virulence factors: A novel approach to pancreatic cancer diagnosis – Xuemin Zeng – Biomolecules & Biomedicine

The Gut Microbiome: A Primer for the Clinician – Olga C Aroniadis – The American Journal of Gastroenterology

Exploring the role of gut microbiota in migraine risk: a two-sample Mendelian randomization study – Xiangyue Meng – Scandinavian Journal of Gastroenterology

High-Throughput Combined Analysis of Saliva Microbiota and Metabolomic Profile in Chinese Periodontitis Patients: A Pilot Study – Jing Ding – Inflammation

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research – Jonathan L Golob – Cell Reports. Medicine

Impact of dietary inflammatory index on gingival health – Roberta Andrade Reis – Journal of Periodontology

Air particulate pollution exposure associated with impaired cognition via microbiota gut-brain axis: an evidence from rural elderly female in northwest China – Jia Yuan – Environmental Science and Pollution Research International

Metabolic flux and catabolic kinetics of prebiotic-like dietary polyphenol phlorizin in association with gut microbiota in vitro – Jiang Chen – Food Chemistry

Review: Genital tract microbiota composition profiles and use of prebiotics and probiotics in gynaecological cancer prevention: review of the current evidence, the European Society of Gynaecological Oncology prevention committee statement – Anita Mitra – The Lancet. Microbe

Review: Wound Microbiota and Its Impact on Wound Healing – Małgorzata Zielińska – International Journal of Molecular Sciences

Review: Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem – Shuang Wang – Gut Microbes

Animal Model Studies

Gut microbiome responds to alteration in female sex hormone status and exacerbates metabolic dysfunction – Tzu-Wen L Cross – Gut Microbes

Oral fecal transplantation enriches Lachnospiraceae and butyrate to mitigate acute liver injury – Chun-Ju Yang – Cell Reports 

Impact of various high fat diets on gene expression and the microbiome across the mouse intestines – Jose Martinez-Lomeli – Scientific Reports

Non-Model Animal Microbiome

Characteristics of gut microbiota in captive Asian elephants (Elephas maximus) from infant to elderly – Sarisa Klinhom – Scientific Reports

Honeybee symbiont Bombella apis could restore larval-to-pupal transition disrupted by antibiotic treatment – Chen Xiaowen – Journal of Insect Physiology

Toll receptor ligand Spätzle 4 responses to the highly pathogenic Enterococcus faecalis from Varroa mites in honeybees – Wenhao Zhang – PLoS Pathogens

Plant Microbiome

Review: Unveiling the significance of rhizosphere: Implications for plant growth, stress response, and sustainable agriculture – Wogene Solomon – Plant Physiology and Biochemistry

Environmental Microbiome

Connecting molecular biomarkers, mineralogical composition, and microbial diversity from Mars analog lava tubes – Vera Palma – The Science of the Total Environment

The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome – Ate H Jaarsma – Frontiers in Microbiology

Review: A global review on the abundance and threats of microplastics in soils to terrestrial ecosystem and human health – Wenshan Shi – The Science of the Total Environment

Microbiome analysis: tools, techniques and resources

VIBES: A consensus subtyping of the vaginal microbiota reveals novel classification criteria – Diego Fernández-Edreira – Computational and Structural Biotechnology Journal

Generalized matrix decomposition regression: estimation and inference for two-way structured data – Yue Wang – The Annals of Applied Statistics

Single-cell and spatiotemporal transcriptomic analyses reveal the effects of microorganisms on immunity and metabolism in the mouse liver – Ruizhen Zhao – Computational and Structural Biotechnology Journal

PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions – David Vorländer – Biotechnology and Bioengineering

Mock microbial community meta-analysis using different trimming of amplicon read lengths – Diana Haider – Environmental Microbiology

Review: In Vitro Models for Investigating Intestinal Host-Pathogen Interactions – Reece McCoy – Advanced Science

December 23, 2023

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Happy Holidays, from the MicrobiomeDigest team!

Human and General Microbiome

Gut microbiota predicts severity and reveals novel metabolic signatures in acute pancreatitis – Christoph Ammer-Herrmenau – Gut

Human gut microbiota from hepatitis B virus-infected individuals is associated with reduced triglyceride level in mice: faecal transplantation study – Han-Na Kim – Microbes and Infection

Commensal bacteria maintain a Qa-1(b)-restricted unconventional CD8(+) T population in gut epithelium – Jian Guan – eLife

Akkermansia muciniphila – friend or foe in colorectal cancer? – Ekaterina O Gubernatorova – Frontiers in Immunology

Association between erythrocyte membrane fatty acids and gut bacteria in obesity-related cognitive dysfunction – Tong Zhao – AMB Express

Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV – Shilpa Ray – NPJ Biofilms and Microbiomes

The relationship between sleep, gut microbiota, and metabolome in patients with depression and anxiety: A secondary analysis of the observational study – Arisa Tanaka – PloS ONE

Persistence of gut dysbiosis in individuals with anorexia nervosa – Yukiko Morisaki – PloS ONE

Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji – Sankhya Bommana – mBio

Gut microbiome-based machine learning for diagnostic prediction of liver fibrosis and cirrhosis: a systematic review and meta-analysis – Xiaopei Liu – BMC Medical Informatics and Decision Making

Targeting gut microbial nitrogen recycling and cellular uptake of ammonium to improve bortezomib resistance in multiple myeloma – Yinghong Zhu – Cell Metabolism

Variations in the oral microbiome and metabolome of methamphetamine users – Dawei Wang – mSystems

Investigating the causal impact of gut microbiota on glioblastoma: a bidirectional Mendelian randomization study – Chuan Zeng – BMC Genomics

Alterations of oral and gut viromes in hypertension and/or periodontitis – Hui-Lin Ye – mSystems

Heterogeneous associations of gut microbiota with Crohn’s disease activity – Susanne Pinto – Gut Microbes

Early / Infant / Children Microbiome

Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children – Kevin S Bonham – Science Advances

The association of tonsillar microbiota with biochemical indices based on obesity and tonsillar hypertrophy in children – Jiwon Park – Scientific Reports

Synergistic horizontal transfer of antibiotic resistance genes and transposons in the infant gut microbial genome – Yanwen Ding – mSphere

Beneficial Microbes and Compounds

Potential therapeutic implications of histidine catabolism by the gut microbiota in NAFLD patients with morbid obesity – Sergio Quesada-Vázquez – Cell Reports Medicine

Attenuation of allergen-specific immunotherapy for atopic dermatitis by ectopic colonization of Brevundimonas vesicularis in the intestine – Xiaochun Liu – Cell Reports Medicine

Model and Non-Model Animal Microbiome

The influence of diet on gut microbiome and body mass dynamics in a capital-breeding migratory bird – Isabelle Jones – PeerJ

Autophagic dysfunction and gut microbiota dysbiosis cause chronic immune activation in a Drosophila model of Gaucher disease – Magda L Atilano – PLoS Genetics

Cytolethal distending toxin B inoculation leads to distinct gut microtypes and IBS-D-like microRNA-mediated gene expression changes in a rodent model – Gabriela Leite – Gut Microbes

Microbiome and Evolution

Evolutionary patterns and processes in animal microbiomes – Florent Mazel – Journal of Evolutionary Biology

Plant and Soil Microbiome

Wheat fungal endophyte communities are inseparable from the host and influence plant development – Or Sharon – mBio

Environmental Microbiome

Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments – Yingyu Bao – Environmental Science & Technology

Microbiome Analysis: Tools, Techniques and Resources

Review: Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology – Corinne Walsh – mBio

SOHPIE: Statistical Approach via Pseudo-Value Information and Estimation for Differential Network Analysis of Microbiome Data – Seungjun Ahn – Bioinformatics

Examining the functional space of gut microbiome-derived peptides – Ying-Chiang J Lee – MicrobiologyOpen

A new absolute quantitative method for peptide and metabolite detection – Carlo Brogna – Journal of Mass Spectrometry

Next steps in studying host-microbiome interactions in apical periodontitis – Athina C Georgiou – Frontiers in Oral Health

December 18, 2023

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Human and General Microbiome

Microbiome diversity protects against pathogens by nutrient blocking – Frances Spragge – Science 

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients – Zixuan Xie – Microbiome

Functional alterations and predictive capacity of gut microbiome in type 2 diabetes – Nihar Ranjan Dash – Scientific Reports

Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection – Christopher J Lehmann – Cell Host & Microbe

Establishment of oral microbiome in very low birth weight infants during the first weeks of life and the impact of oral diet implementation – Pedro A R Vanzele – PloS One

Infant gut DNA bacteriophage strain persistence during the first 3 years of life – Yue Clare Lou – Cell Host & Microbe

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition – Elias R Gerrick – Cell

Poly-omic risk scores predict inflammatory bowel disease diagnosis – Christopher H Arehart – mSystems

Review: Impact of glyphosate (Roundup(TM)) on the composition and functionality of the gut microbiome – Lauren Walsh – Gut Microbes

Rapid turnover and short-term blooms of Escherichia coli in the human gut – Na Han – Journal of Bacteriology

Designing a multi-epitope vaccine against Peptostreptococcus anaerobius based on an immunoinformatics approach – Yudan Mao – Synthetic and Systems Biotechnology

Twnbiome: a public database of the healthy Taiwanese gut microbiome – Amrita Chattopadhyay – BMC Bioinformatics

Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting – Alessandra Riva – Nature Communications

Review: Application of omics technologies in cariology research: A critical review with bibliometric analysis – Josie Shizhen Zhang – Journal of Dentistry

Dysbiosis and associated stool features improve prediction of response to biological therapy in inflammatory bowel disease – Clara Caenepeel – Gastroenterology

Highlight: Female Reproductive Tract Microbiome

Review: Culturomics in Unraveling the Upper Female Reproductive Tract Microbiota – Robin Vanstokstraeten – Seminars in Reproductive Medicine

A manifold-based framework for studying the dynamics of the vaginal microbiome – Mor Tsamir-Rimon – NPJ Biofilms and Microbiomes

Culturomics reveals a hidden world of vaginal microbiota with the isolation of 206 bacteria from a single vaginal sample – Linda Abou Chacra – Archives of Microbiology

Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses – Tanya Kumar – Microbiology Spectrum

Non-Model Animal Microbiome

Activity budget and gut microbiota stability and flexibility across reproductive states in wild capuchin monkeys in a seasonal tropical dry forest – Shasta E Webb – Animal Microbiome

Validation of method for faecal sampling in cats and dogs for faecal microbiome analysis – Xavier Langon – BMC Veterinary Research

Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations – Amalia Bogri – mSystems

Plant and Soil Microbiome

Fungal community composition changes and reduced bacterial diversity drive improvements in the soil quality index during arable land restoration – Pingxing Wan – Environmental Research

Two-for-one: root microbiota orchestrates both soil pH and plant nutrition – João Antonio Siqueira – Trends in Plant Science

Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum – Rhea Aqueel – NPJ Biofilms and Microbiomes

Environmental Microbiome

Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort – Guido Bonthond – ISME Communications

Increased prokaryotic diversity in the Red Sea deep scattering layer – Tamara Megan Huete-Stauffer – Environmental Microbiome

December 10, 2023

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General and Human Microbiome

Altered gut microbiome associated with metabolic-associated fatty liver disease in Chinese children – Jing Ji – Clinical Nutrition (Edinburgh, Scotland)

Airway environment drives the selection of quorum sensing mutants and promote Staphylococcus aureus chronic lifestyle – Xiongqi Ding – Nature Communications

Review: Gut microbiota in overweight and obesity: crosstalk with adipose tissue – Patrice D Cani – Nature Reviews. Gastroenterology & Hepatology

Review: Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment – Muhamad Aidilfitri Mohamad Roslan – NPJ Biofilms and Microbiomes

Metaproteomic assessment of gut microbial and host functional perturbations in Helicobacter pylori-infected patients subjected to an antimicrobial protocol – Marcello Abbondio – Gut Microbes

The facial microbiome and metabolome across different geographic regions – Rong Tao – Microbiology Spectrum

Periodontitis salivary microbiota exacerbates colitis-induced anxiety-like behavior via gut microbiota – Jun Qian – NPJ Biofilms and Microbiomes

Vasoactive intestinal polypeptide plays a key role in the microbial-neuroimmune control of intestinal motility – Xiaopeng Bai – Cellular and Molecular Gastroenterology and Hepatology

Multi-omics analyses reveal bacteria and catalase associated with keloid disease – Mengjie Shan – EBioMedicine

Beneficial Microbes and Compounds

Genomic and Phenotypic Insight into the Probiotic Potential of Lactic Acid Bacterial spp. Associated with the Human Gut Mucosa – Kanwal Aziz – Probiotics and Antimicrobial Proteins

Review: A review on the use of prebiotics in ulcerative colitis – James M Kennedy – Trends in Microbiology

Oral magnesium prevents acetaminophen-induced acute liver injury by modulating microbial metabolism – Dongping Li – Cell Host & Microbe

Review: Akkermansia muciniphila and Alcohol-Related Liver Diseases. A Systematic Review – Lydie Sparfel – Molecular Nutrition & Food Research

Review: Triangulating nutrigenomics, metabolomics and microbiomics toward personalized nutrition and healthy living – George Lagoumintzis – Human Genomics

Non-Model Animal Microbiome 

The role of diet and host species in shaping the seasonal dynamics of the gut microbiome – Claire E Williams – FEMS Microbiology Ecology

Increased environmental microbial diversity reduces the disease risk of a mosquitocidal pathogen – Zhiwei Kang – mBio

Plant and Soil Microbiome

Characterization of microbial contamination in agricultural soil: A public health perspective – Xiaodi Li – The Science of the Total Environment

Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community – Matevž Likar – Scientific Reports

Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease – Yanyan Zhou – Nature Communications

Environmental Microbiome

Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity – Yang Chen – NPJ Biofilms and Microbiomes

Multiple spatial scales of bacterial and fungal structural and functional traits affect carbon mineralization – Zhiyuan Ma – Molecular Ecology

Microbiome Analysis: tools, techniques and resources

Review: Establishing genetic manipulation for novel strains of human gut bacteria – Paul O Sheridan – Microbiome Research Reports

November 27, 2023

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Human and General Microbiome

Multi-site microbiota alteration is a hallmark of kidney stone formation – Kait F Al – Microbiome

Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study – Asha Yadav – Journal of Applied Microbiology

Trans-vaccenic acid reprograms CD8(+) T cells and anti-tumour immunity – Hao Fan – Nature

Multi-omics analysis of hospital-acquired diarrhoeal patients reveals biomarkers of enterococcal proliferation and Clostridioides difficile infection – Marijana Bosnjak – Nature Communications

Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador – Kelsey J Jesser – Gut Microbes

Gut microbiome and frailty: insight from genetic correlation and mendelian randomization – Guanghui Cui – Gut Microbes

Review: Metabolic exchanges are ubiquitous in natural microbial communities – Christian Kost – Nature Microbiology

Review: Evolution of a Pathogenic Microbiome – Pui Yin Wong – Journal of Clinical Medicine

Review: Evidence for the contribution of the gut microbiome to obesity and its reversal – Douwe F de Wit – Science Translational Medicine

Beneficial Microbes and Compounds

Parabacteroides distasonis ameliorates insulin resistance via activation of intestinal GPR109a – Yonggan Sun – Nature Communications

Galactooligosaccharide Mediates NF-κB Pathway to Improve Intestinal Barrier Function and Intestinal Microbiota – Menglu Xi – Molecules 

A self-stabilized and water-responsive deliverable coenzyme-based polymer binary elastomer adhesive patch for treating oral ulcer – Chunyan Cui – Nature Communications

A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation – Chengcheng Zhang – Cell Host & Microbe

Meta-analysis: Fiber intake and fiber intervention in depression and anxiety: a systematic review and meta-analysis of observational studies and randomized controlled trials – Hajara Aslam – Nutrition Reviews

Animal Microbiome

Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius – Haoyu Lang – Nature Communications

A coral-associated actinobacterium mitigates coral bleaching under heat stress – Jie Li – Environmental Microbiome

Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations – Jennifer L Matthews – Scientific Reports

Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts – Dan Sun – ISME Communications

Experimental mining plumes and ocean warming trigger stress in a deep pelagic jellyfish – Vanessa I Stenvers – Nature Communications

Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis – Karina Gutiérrez-García – ISME Communications

Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape – Huan-Huan Liu – Microbial Ecology

Animal Model Microbiome

Gut microbiota-bile acid crosstalk regulates murine lipid metabolism via the intestinal FXR-FGF19 axis in diet-induced humanized dyslipidemia – Hongtao Xu – Microbiome

Multi-omics data reveals aberrant gut microbiota-host glycerophospholipid metabolism in association with neuroinflammation in APP/PS1 mice – Xiaohang Qian – Gut Microbes

Plant and Environmental Microbiome

Combined application of microbial inoculant and kelp-soaking wastewater promotes wheat seedlings growth and improves structural diversity of rhizosphere microbial community – Xin Song – Scientific Reports

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments – Yajun Yang – Scientific Reports

Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost – Karl J Romanowicz – ISME Communications

Microbiome Analysis: tools, techniques, and resources

PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies – Vincenzo Bonnici – Journal of Biomedical Informatics

PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model – Jun Wu – Bioinformatics

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes – Shreya Arya – PNAS

Vaccinomics-aided next-generation novel multi-epitope-based vaccine engineering against multidrug resistant Shigella sonnei: Immunoinformatics and chemoinformatics approaches – Sara Aiman – PloS One

Detecting host responses to microbial stimulation using primary epithelial organoids – Jette Bornholdt – Gut Microbes

Review: Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities – Suleiman Aminu – Critical Reviews in Microbiology

November 20, 2023

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Human and General Microbiome

Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure – Abigail L Zeamer – Translational Psychiatry

The preterm human milk microbiota fluctuates by postpartum week and is characterized by gestational age and maternal BMI – Evgenia Jen Filatava – mBio

Strain-resolved metagenomic analysis of the gut as a reservoir for bloodstream infection pathogens among premature infants in Singapore – Sarah M Heston – Gut Pathogens

Porphyromonas gingivalis as a promotor in the development of the alcoholic liver disease via ferroptosis – Chao Yao – Microbes and Infection

The core phageome and its interrelationship with preterm human milk lipids – Wen C Yew – Cell Reports

Longitudinal analysis at three oral sites links oral microbiota to clinical outcomes in allogeneic hematopoietic stem-cell transplant – Vitor Heidrich – Microbiology Spectrum

Gut inflammation associated with age and Alzheimer’s disease pathology: a human cohort study – Margo B Heston – Scientific Reports

Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia – Emmanuel Montassier – Nature Medicine

Beneficial Microbes and Compounds

Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra – Andrew M King – Nature Microbiology

Skin benefits of postbiotics derived from Micrococcus luteus derived from human skin: an untapped potential for dermatological health – Young Mok Heo – Genes & Genomics

Akkermansia muciniphila attenuated lipopolysaccharide-induced acute lung injury by modulating the gut microbiota and SCFAs in mice – Jian Shen – Food & Function

Review: The Potential of Meta-Proteomics and Artificial Intelligence to Establish the Next Generation of Probiotics for Personalized Healthcare – Arpita Das – Journal of Agricultural and Food Chemistry

Review: Gut microbiome in healthy aging versus those associated with frailty – Mi Young Lim – Gut Microbes

Animal Microbiome

Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome – Javad Sadeghi – Microbiome

Aedes aegypti microbiome composition covaries with the density of Wolbachia infection – Jane Pascar – Microbiome

Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis – H Domin – Microbiome

Microbial symbionts are shared between ants and their associated beetles – Catalina Valdivia – Environmental Microbiology

The gut microbiome mediates adaptation to scarce food in Coleoptera – Oana Teodora Moldovan – Environmental Microbiome

Animal Model Microbiome

Interplay of gut microbiota and host epithelial mitochondrial dysfunction is necessary for the development of spontaneous intestinal inflammation in mice – Kibrom M Alula – Microbiome

Environmental Microbiome

Microbial diversity and community structure dynamics in acid mine drainage: Acidic fire with dissolved heavy metals – Wasim Sajjad – The Science of the Total Environment

Polar lake microbiomes have distinct evolutionary histories – Bjorn Tytgat – Science Advances

Plant Microbiome

PSKR1 balances the plant growth-defence trade-off in the rhizosphere microbiome – Siyu Song – Nature Plants

Streptomyces alleviate abiotic stress in plant by producing pteridic acids – Zhijie Yang – Nature Communications

Microbiome Analysis: tools, techniques and resources

The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease – Qinglong Wu – The Journal of Clinical Investigation

Review: Machine learning for microbiologists – Francesco Asnicar – Nature Reviews. Microbiology

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November 6, 2023

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Human Gut Microbiome

Altered Gut Microbiota and Short-chain Fatty Acids in Chinese Children with Constipated Autism Spectrum Disorder – Jianquan He – Scientific Reports

Clostridium butyricum and Clostridium tyrobutyricum: angel or devil for necrotizing enterocolitis? – Ruizhi Tao – mSystems

Gut microbiota composition and diversity before, during, and two months after rifamycin-based tuberculosis preventive therapy – Marie Nancy Séraphin – Scientific Reports

Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species – Jamie English – Journal of Medical Microbiology

Bacterial SNPs in the human gut microbiome associate with host BMI – Liron Zahavi – Nature Medicine

Fecal short-chain fatty acids in non-constipated irritable bowel syndrome: a potential clinically relevant stratification factor based on catabotyping analysis – Giorgio Gargari – Gut Microbes

Characterizing alterations in the gut microbiota following postpartum weight change – Bridget N Chalifour – mSystems

Core-genome multilocus sequence typing and core-SNP analysis of Clostridium neonatale strains isolated in different spatio-temporal settings – Victoria Mesa – Microbiology Spectrum

Human Microbiome (outside the gut)

Identification of root canal microbiota profiles of periapical tissue diseases using matrix-assisted laser desorption/ionization time-of-flight mass spectrometer – Mete Ahlat – Anaerobe

Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome – Márcia Sousa – International Journal of Systematic and Evolutionary Microbiology

Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population – Giacomo Antonello – Scientific Reports

Prolonged mask wearing changed nasal microbial characterization of young adults during the COVID-19 pandemic in Shanghai, China – Guoxiu Xiang – Frontiers in Immunology

Beneficial Microbes, Compounds and Interventions

Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid – Xinyue Yang – NPJ Biofilms and Microbiomes

A gut microbial metabolite of linoleic acid ameliorates liver fibrosis by inhibiting TGF-β signaling in hepatic stellate cells – Nanaho Kasahara – Scientific Reports

Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement – Michael H Woodworth – Science Translational Medicine

Animal Microbiome

Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies – Yanjiao Li – Microbiome

Shifts in the coral microbiome in response to in situ experimental deoxygenation – Rachel D Howard – Applied and Environmental Microbiology

Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model – Tanner G Richie – mSystems

Estradiol mediates colonic epithelial protection in aged mice after stroke and is associated with shifts in the gut microbiome – Juneyoung Lee – Gut Microbes

Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts – Justin Maire – mSystems

Gut bacteria mediated adaptation of diamondback moth, Plutella xylostella, to secondary metabolites of host plants – Xiaofeng Xia – mSystems

Environmental Microbiome

Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere – Vinko Zadjelovic – Microbiome

Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia – Coco Koedooder – mSystems

Review: Microbial ecology of drinking water from source to tap – Leili Abkar – The Science of the Total Environment

Microbiome Analysis: Tools, Techniques and Resources

Food4healthKG: Knowledge graphs for food recommendations based on gut microbiota and mental health – Chengcheng Fu – Artificial Intelligence in Medicine

Testing latent classes in gut microbiome data using generalized Poisson regression models – Xinhui Qiao – Statistics in Medicine

October 30, 2023

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Human and General Microbiome

Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability – Svenja Starke – The ISME Journal

Gut microbiota impacts bone via Bacteroides vulgatus-valeric acid-related pathways – Xu Lin – Nature Communications

The global burden of antimicrobial resistance – urinary tract infections – Sibylle Von Vietinghoff – Nephrology, Dialysis, Transplantation

Class I HLA Allele Predicted Restricted Antigenic Coverages for Fap2 Protein of Fusobacterium nucleatum Are Associated with Colorectal Cancer Incidence – Mustapha Zeddou – Asian Pacific Journal of Cancer Prevention

Microbial-dependent recruitment of immature myeloid cells promotes intestinal regeneration – Zhengyu Jiang – Cellular and Molecular Gastroenterology and Hepatology

Prior antibiotic administration disrupts anti-PD-1 responses in advanced gastric cancer by altering the gut microbiome and systemic immune response – Chang Gon Kim – Cell Reports Medicine

Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts – Janetta Top – Microbiology Spectrum

White-nose syndrome restructures bat skin microbiomes – Meghan Ange-Stark – Microbiology Spectrum

Linking Clinical Blood Metabogram and Gut Microbiota – Petr G Lokhov – Metabolites

A citizen-science-enabled catalogue of the vaginal microbiome and associated factors – Sarah Lebeer – Nature Microbiology

Low-dose ethanol consumption inhibits neutrophil extracellular traps formation to alleviate rheumatoid arthritis – Lin Jin – Communications Biology

Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria – Sophie Robitaille – Nature Ecology & Evolution

Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions – Aitor Blanco-Míguez – Cell Host & Microbe

Gut microbe-metabolite profiles are associated with microbial pathways of longevity in women: a cross-sectional study conducted in China – Qinren Zhang – Gerontology

Longitudinal analysis of vaginal microbiota during IVF fresh embryo transfer and in early pregnancy – Sofia Väinämö – Microbiology Spectrum

Gut microbiota and autism spectrum disorders: where do we stand? – Sa’ed H Zyoud – Gut Pathogens

Host fecal DNA specific methylation signatures mark gut dysbiosis and inflammation in children affected by autism spectrum disorder – Mariella Cuomo – Scientific Reports

Gut microbiome-derived ammonia modulates stress vulnerability in the host – Pei Wang – Nature Metabolism

Nanobodies against C. difficile TcdA and TcdB reveal unexpected neutralizing epitopes and provide a toolkit for toxin quantitation in vivo – Shannon L Kordus – PLoS Pathogens

Review: Microbiome-based therapies for periodontitis and peri-implantitis – Xindi Wei – Oral Diseases

Animal Microbiome

Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats – Yue Dong – Microbiology Spectrum

Integrated multi-omics analysis reveals the positive leverage of citrus flavonoids on hindgut microbiota and host homeostasis by modulating sphingolipid metabolism in mid-lactation dairy cows consuming a high-starch diet – Yuchao Zhao – Microbiome

More Microbes

Review: Update on novel validly published taxa of bacteria isolated from domestic animals described in 2022 – Sara D Lawhon – Journal of Clinical Microbiology

Plant Microbiome

Location: root architecture structures rhizosphere microbial associations – Tania Galindo-Castañeda – Journal of Experimental Botany

Environmental Microbiome

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem – Clement Coclet – Microbiome

Shotgun metagenomics and computational profiling of the plastisphere microbiome: unveiling the potential of enzymatic production and plastic degradation – Mahnoor Saleem – Archives of Microbiology

Microbiome Analysis: Tools, Techniques and Resources

Machine-learning analysis of cross-study samples according to the gut microbiome in 12 infant cohorts – Petri Vänni – mSystems

Analyzing microbial evolution through gene and genome phylogenies – Sarah Teichman – Biostatistics

AnimalMetaOmics: a multi-omics data resources for exploring animal microbial genomes and microbiomes – Ruirui Hu – Nucleic Acids Research

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource – Thomas S B Schmidt – Nucleic Acids Research

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool – Hoon Je Seong – Briefings in Bioinformatics

dbAPIS: a database of anti-prokaryotic immune system genes – Yuchen Yan – Nucleic Acids Research

Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis – Sinan U Umu – GigaScience

aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow – Zoé Pochon – Genome Biology

October 23, 2023

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Human and General Microbiome

Secretory IgA impacts the microbiota density in the human nose – Rob van Dalen – Microbiome

Disease-specific loss of microbial cross-feeding interactions in the human gut – Vanessa R Marcelino – Nature Communications

Feasibility of a dietary intervention to modify gut microbial metabolism in patients with hematopoietic stem cell transplantation – Mary M Riwes – Nature Medicine

Four functional profiles for fibre and mucin metabolism in the human gut microbiome – Simon Labarthe – Microbiome

The airway microbiota of neonates colonized with asthma-associated pathogenic bacteria – Jonathan Thorsen – Nature Communications

Multiomic profiling of cutaneous leishmaniasis infections reveals microbiota-driven mechanisms underlying disease severity – Camila Farias Amorim – Science Translational Medicine

Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring – Lauren E Colbert – Cancer Cell

Analysis of the influence of host lifestyle (coffee consumption, drinking, and smoking) on Korean oral microbiome – Kyeong-Min Yu – Forensic Science International. Genetics

Potential roles of gut microbiota in metal mixture and bone mineral density and osteoporosis risk association: an epidemiologic study in Wuhan – Jianli Zhang – Environmental Science and Pollution Research International

Characteristics of gut microbiota and metabolic phenotype in patients with major depressive disorder based on multi-omics analysis – Xianpeng Zu – Journal of Affective Disorders

The role of microbial interactions in dental caries: Dental plaque microbiota analysis – Qingyi Shao – Microbial Pathogenesis

A distinctive subgingival microbiome in patients with periodontitis and Alzheimer’s disease compared with cognitively unimpaired periodontitis patients – Hee Sam Na – Journal of Clinical Periodontology

Review: On developmental programming of the immune system – Jun Young Hong – Trends in Immunology

Review: Regulation of pain perception by microbiota in Parkinson’s Disease – Zulmary Manjarres – Pharmacological Reviews

Review: Single-cell analysis and spatial resolution of the gut microbiome – Bhoomi Madhu – Frontiers in Cellular and Infection Microbiology

Beneficial Microbes and Compounds

Synbiotic Sapota-do-Solimões (Quararibea cordata Vischer) Juice Improves Gut Microbiota and Short-Chain Fatty Acid Production in an In Vitro Model – Rhonyele Maciel da Silva – Probiotics and Antimicrobial Proteins

Limosilactobacillus fermentum HF06-derived paraprobiotic and postbiotic alleviate intestinal barrier damage and gut microbiota disruption in mice with ulcerative colitis – Chunhong Liu – Journal of the Science of Food and Agriculture

Animal Microbiome (including Animal Models)

A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs – Mirja Thomsen – Microbiome

High soluble fiber promotes colorectal tumorigenesis through modulating gut microbiota and metabolites in mice – Jia Yang – Gastroenterology

Gut bacterial consortium enriched in a biofloc system protects shrimp against Vibrio parahaemolyticus infection – Haipeng Guo – Microbiome

Environmental Microbiome

Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls – Tamara Martin-Pozas – Microbiological Research

Review: The interplay between microbial communities and soil properties – Laurent Philippot – Nature Reviews. Microbiology

Plant Microbiome

Insights into accumulation of active ingredients and rhizosphere microorganisms between Salvia miltiorrhiza and S. castanea – Zishu Xu – FEMS Microbiology Letters

Microbiome and Evolution

Review: Hierarchical eco-evo dynamics mediated by the gut microbiome – Ellen Decaestecker – Trends in Ecology & Evolution

October 16, 2023

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Human and General Microbiome

A Sedentary Lifestyle Changes the Composition and Predicted Functions of the Gut Bacterial and Fungal Microbiota of Subjects from the Same Company – Longwei Xu – Current Microbiology

Animal Microbiome

Effect of urbanization and parasitism on the gut microbiota of Darwin’s finch nestlings – Gabrielle Solomon – Molecular Ecology

Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites – Lucas G Huggins – Molecular Ecology Resources

Bacterial networks in Atlantic salmon with Piscirickettsiosis – Yoandy Coca – Scientific Reports

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions that respond to ovulation regulation in the mouse endometrium – Sisi Pu – BMC Genomics

Beneficial Microbes, Foods and Compounds

Probiotic-fermented tomato alleviates high-fat diet-induced obesity in mice: Insights from microbiome and metabolomics – Benliang Wei – Food Chemistry

Lactobacillus rhamnosus Modulates Lung Inflammation and Mitigates Gut Dysbiosis in a Murine Model of Asthma-COPD Overlap Syndrome – Jéssica Aparecida Vasconcelos – Probiotics and Antimicrobial Proteins

Fermented Goat’s Milk Contributes to the Recovery of Iron Deficiency Anemia via Modulation of the Gut Microbiome – Ana Soriano-Lerma – Journal of Agricultural and Food Chemistry

Environmental Microbiome

Coexistence of specialist and generalist species within mixed plastic derivative-utilizing microbial communities – Laura Schaerer – Microbiome

Review: A critical review of the recent trends in source tracing of microplastics in the environment – Kiruthika K M – Environmental Research

Keystone taxa of phoD-harboring bacteria mediate alkaline phosphatase activity during biochar remediation of Cd-contaminated soil – Qiang Wang – The Science of the Total Environment

Plant Microbiome

Maintaining beneficial alga-associated bacterial communities under heat stress: Insights from controlled co-culture experiments using antibiotic-resistant bacterial strains – Elham Karimi – FEMS Microbiology Ecology

Review: Deep discovery informs difficult deployment in plant microbiome science – Dor Russ – Cell

Highlights: Plant cell wall component induced bacterial development – Ákos T Kovács – Trends in Microbiology

Microbiome Analysis: Tools, Techniques and Resources

MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile – Pieter-Jan Van Camp – Microbiome

Subgroup Identification Using Virtual Twins for Human Microbiome Studies – Hyunwook Koh – IEEE/ACM Transactions on Computational Biology and Bioinformatics