Monthly Archives: December 2023

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 15, 2023

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Today’s digest features house mice gut microbiome, infant gut DNA bacteriophage strain persistence, maternal gut microbiome in pregnancy, and more.

Do not miss Francine Marques’s opinion on rethinking culture to unlock the potential of research.

See you at #MVIF next week!

Respiratory microbiome

Review: Winds of change a tale of: asthma and microbiome – David Galeana-Cadena – Frontiers in Microbiology

Gut microbiome

Review: The maternal gut microbiome in pregnancy: implications for the developing immune system – Omry Koren – Nature Reviews Gastroenterology & Hepatology

Bioactive glycans in a microbiome-directed food for children with malnutrition – Matthew C. Hibberd – Nature

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

Gut microbiota-related metabolite alpha-linolenic acid mitigates intestinal inflammation induced by oral infection with Toxoplasma gondii – Jing Yang – Microbiome

Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont – Peter Kuffa – Cell Host & Microbe

Animal microbiome

Subspecies divergence, hybridisation and the spatial environment shape phylosymbiosis in the microbiome of house mice – Susana C. M. Ferreira – bioRxiv

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers – Gilles L. C. Baud – Genome Biology

Seasonal and environmental factors contribute to the variation in the gut microbiome: a large-scale study of a small bird – Martta Liukkonen – bioRxiv

Plant-Root-Soil microbiome

Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota – Nathan Vannier – Nature Communications

Virome

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

Techniques

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities – Patrick Müller – Nature Protocols

Bioinformatics

MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes – James P.J. Chong – bioRxiv

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

December 6, 2023

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Human salivary microbiome

Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer – de Medeiros et al. – Microbiome

Human skin microbiome

[PREPRINT]Commensal skin bacteria exacerbate inflammation and delay skin healing – Khadka et al. – bioRxiv

Human vaginal microbiome

Integrating compositional and functional content to describe vaginal microbiomes in health and disease – Holm et al. – Microbiome

Comparison of vaginal microbiota between women with inflammatory bowel disease and healthy controls – Bar et al. – PLOS One

Human gut microbiome

Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics – Deng et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Vitamin D modulation of brain-gut-virome disorder caused by polystyrene nanoplastics exposure in zebrafish (Danio rerio) – Teng et al – Microbiome

Animal microbiome (for animals in the wild)

Diversity of gut microbiome in Rocky Mountainsnail across its native range – Chalifour, Elder & Li – PLOS One

[PREPRINT]Testing the effectiveness of a commercially sold probiotic on restoring the gut microbiota of honey bees: a field study – Damico et al. – bioRxiv

Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations – Lin et al. – Microbiome

Plant, root, and soil microbiome

Effects of multiple N, P, and K fertilizer combinations on strawberry growth and the microbial community – Bai et al. – PLOS One

Comparison of microbial community assemblages in the rhizosphere of three Amaranthus spp. – Chee-Sanford & Connor – PLOS One

Bioinformatics

Phantom oscillations in principal component analysis – Shinn – PNAS
This phenomenon is not new (e.g. know as horseshoe effect) but Shinn gives a very understandable explanation.

The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples – Heupink et al. – PLOS Computational Biology

[PREPRINT]metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis – Sun et al. – bioRxiv

[PREPRINT]MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics – Ma, Thairu & Sankaran