Category Archives: Animal experiments

December 6, 2024

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Gut Microbiome

Protection against Clostridioides difficile disease by a naturally avirulent strain – Dong et al. Cell Host & Microbe

Animal experiments 

The host genotype actively shapes its microbiome across generations in laboratory mice – Benga et al. Microbiome

Prenatal antibiotics reduce breast milk IgA and induce dysbiosis in mouse offspring, increasing neonatal susceptibility to bacterial sepsis – Pietrasanta et al. Cell Host & Microbe

Oral and respiratory microbiomes

Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner – Jaber et al. npj biofilms and microbiomes

Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies – Kim et al. Communications biology

The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children – Kristensen et al. Cell Reports Medicine

Plant and environmental microbiomes

Plant microbiota feedbacks through dose-responsive expression of general non-self response genes – Keppler et al. Nature Plants

Dynamics of rice seed-borne bacteria from acquisition to seedling colonization – Chen et al. Microbiome

Bioinformatics

Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets – Bradford et al. BMC Bioinformatics

[PREPRINT] TaxSEA: an R package for rapid interpretation of differential abundance analysis output – Ryan. bioRxiv 

November 29, 2024

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NEWS: ” Researchers say the social-media platform — an alternative to X — offers more control over the content they see and the people they engage with.” Source: https://www.nature.com/articles/d41586-024-03784-6

INVITATION: MVIF’s last event of the year is coming up! Quick, register now :https://cassyni.com/s/mvif-34
Looking forward to seeing you next week!

It's Wednesday! …and #MVIF 34 program is out! 🤩⭐️MicroTalks: 🇹🇼 Ha T. Doan🇦🇺 Vedanth Ramji⭐️ Keynote: 🇺🇸 Sean Gibbons @gibbological.bsky.social ⭐️Selected talks: 🇯🇵 Yuya Kiguchi🇦🇺 Kurtis Budden🇨🇭 Amit Halkhoree (#Roche)Registration: cassyni.com/s/mvif-34

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2024-11-20T08:57:41.034Z

Citizen science

Citizen science as an instrument for women’s health research – Sarah Ahannach – Nature Medicine 

General

Perspective: A framework for understanding collective microbiome metabolism – Matthias Huelsmann – Nature Microbiology 

Thrilled to announce that Matthias Hülsmann's new perspective is now out in @naturemicrobiol.bsky.social! This exciting work is shaping how our group thinks about collective microbiome metabolism. Check it out! http://www.nature.com/articles/s41…

— Microbial Systems Ecology Lab (@micsysecolab.bsky.social) 2024-11-26T12:45:51.587Z

Gut microbiome

Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome –  Tatiana Borodovich – bioRxiv

Gut microbiota markers in early childhood are linked to farm living, pets in household and allergy – Annika Ljung – Plos One

Gut physiology and environment explain variations in human gut microbiome composition and metabolism – Nicola Procházková – Nature Microbiology

Today we publish an (in my opinion) important paper in @naturemicrobiol.bsky.social 🍾 showing that gut physiology and environment are factors explaining substantial variations in human gut #microbiome composition and #metabolism🦠Fantastic work Procházková et al. 👏www.nature.com/articles/s41…

— Henrik M. Roager (@hroager.bsky.social) 2024-11-27T10:36:53.274Z

Significant difference in gut microbiota Bifidobacterium species but not Lactobacillus species in colorectal cancer patients in comparison with healthy volunteers using quantitative real-time PCR – Fahime Esfandiari – Plos One

Gut microbiome strain-sharing within isolated village social networks – Francesco Beghini – Nature

Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts – Paolo Manghi – Nature Microbiology 

🥁 New Publication Alert:Our manuscript on the ☕️ and #microbiome relationship is out in #NatureMicrobiology:www.nature.com/articles/s41…1/12

— Segata Lab (@cibiocm.bsky.social) 2024-11-18T11:24:44.554Z

Respiratory microbiome

Insights into respiratory microbiome composition and systemic inflammatory biomarkers of bronchiectasis patients – Aleksandras Konovalovas – Clinical Microbiology

Urinary microbiome

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection – Michael L. Neugent – bioRxiv

Distinct maternofetal immune signatures delineate preterm birth onset following urinary tract infection – Samantha Ottinger – bioRxiv

Glucose alters the evolutionary response to gentamicin in uropathogenic Escherichia coli – Shalini Choudhary – bioRxiv

🚨 New preprint 🚨 With two excellent students Shalini Choudhary and Jacob Smith, we started looking at how the metabolic microenvironment of the urinary tract might affect uropathogenic E. coli evolution and response to antibiotics.www.biorxiv.org/content/10.1…

— Rebecca J Hall (@drrebeccajhall.bsky.social) 2024-11-27T08:11:55.853Z

Animal microbiome

Ileal microbial microbiome and its secondary bile acids modulate susceptibility to nonalcoholic steatohepatitis in dairy goats – Yue Wang – Microbiome

Effects of prebiotic and multispecies probiotic supplementation on the gut microbiota, immune function, and growth performance of weaned piglets – Soimer Omar Baldera Huaman – Plos One

Animal and model experiments

Western diet promotes endometriotic lesion growth in mice and induces depletion of Akkermansia muciniphila in intestinal microbiota – Guillaume Parpex – BMC Medicine 

In vitro validation of colon delivery of vitamin B2 through a food grade multi-unit particle system – R.E. Steinert – Beneficial Microbes

Development of a novel complex inflammatory bowel disease mouse model: Reproducing human inflammatory bowel disease etiologies in mice – Sun-Min Seo – Plos One

Marine microbiome

Applications of marine microbial community models in the nature-based economy – Semidán Robaina-Estévez and Jay Gutiérrez – Plos Sustainability and Transformation

Soil microbiome

Soil microbiomes show consistent and predictable responses to extreme events – Christopher G. Knight – Nature

Bioinformatics

A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics – Ye Peng- Cell Host & Microbe

Lefser: Implementation of metagenomic biomarker discovery tool, LEfSe, in R – Asya Khleborodova – Bioinformatics

Technique

Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection – Srinithi Purushothaman – Scientific Reports

#microbiome starter pack 1 & 2 by @claesengroup.bsky.social:—-bsky.app/starter-pack…bsky.app/starter-pack…#human #microbiome starter pack by @ruairirobertson.bsky.social:—bsky.app/starter-pack…#MVIF starter pack by @microbiomevif.bsky.social:—-bsky.app/start/did:pl…

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2024-11-21T21:55:47.051Z

November 8, 2024

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Get ready for #MVIF 33 & register here https://cassyni.com/s/mvif-33
See you next week!


Ecology and evolution

Community conservatism is widespread throughout microbial phyla and environments – Lukas Malfertheiner – bioRxiv 

Gut microbiome

Fecal microbiota transplantation alters the proteomic landscape of inflammation in HIV: identifying bacterial drivers – Claudio Díaz-García – Microbiome

Insights into the gut microbiome of vitiligo patients from India – Sudhir Kumar – BMC Microbiology

Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome – Kevin Whelan – Nature Microbiology

Pregnancy and Early Life Gut Microbiome: Influencing Factors and Health Implications – Trishla Sinha – Research Square

Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma in situ, and healthy women – Emma McCune – mSystems

Gut microbiota regulates stress responsivity via the circadian system – Gabriel S.S. Tofani – Cell Metabolism

Link to the post: https://twitter.com/gabriel_tofani/status/1853862878870446530

Oral microbiome

The role of the oral microbiota in the causal effect of adjunctive antibiotics on clinical outcomes in stage III–IV periodontitis patients – Sven Kleine Bardenhorst – Microbiome

Vaginal microbiome

Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study – Chloe Hicks – BJOG: An International Journal of Obstetrics and Gynaecology

Evaluation of the Vaginal Panel Realtime PCR kit (Vircell, SL) for diagnosing vaginitis: A comparative study with routinely used diagnostics – Isabel Amor – PlosOne

Animal experiments

The gut microbiome in patients with Cushing’s disease affects depression- and anxiety-like behavior in mice – Ding Nie – Microbiome

Food microbiome

Review: Novel fermentations integrate traditional practice and rational design of fermented-food microbiomes – Dillon Arrigan – Current Biology

In-depth characterization of food and environmental microbiomes across different meat processing plants – Coral Barcenilla – Microbiome

Bioinformatics

Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases – Sriram Ramesh – PlosOne 

Techniques

DNA Extraction Protocols for Animal Fecal Material on Blood Spot Cards – Ann-Katrin Llarena – bioRxiv

Link to the post: https://twitter.com/svetlana_up/status/1854091197498683755
Link to the presentation: https://github.com/SvetlanaUP/presentations/blob/main/How_to_give_a_good_online_presentation_11_2024.pdf

October 18, 2024

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Human microbiome

Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery  – Boukadida et al  – Microbiome 

Vaginal lactobacilli produce anti-inflammatory β-carboline compounds – Glick et al – Cell Host & Microbe

An ancient ecospecies of Helicobacter pylori  – Tourrette et al – Nature

Review – Intestinal fungal-host interactions in promoting and maintaining health – Hill & Round – Cell Host & Microbe

Review – Gut microbiome and health: mechanistic insights – de Vos et al – Gut

Animal microbiome

Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health – de Leon et al – Nature Microbiology

Stress triggers irritable bowel syndrome with diarrhea through a spermidine-mediated decline in type I interferon – Zhang et al – Cell Metabolism

Built environment

Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments  – Tong et al – Microbiome 

Plant microbiome

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations  – de Celis et al – Microbiome

Viruses

Using artificial intelligence to document the hidden RNA virosphere – Cell – Hou et al.

Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae – Rotman et al – Cell Host & Microbe

Bioinformatics

SurvBal: Compositional microbiome balances for survival outcomes – Li et al – Bioinformatics

q2-metnet: QIIME2 package to analyze 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota – Balzerani et al – Bioinformatics 

Non-microbiome

News feature – Your diet can change your immune system — here’s how – Nature

October 10, 2024

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Pregnancy and early life

Maternal and infant microbiome and birth anthropometry – Padiyar et al. – iScience

Human oral microbiome

Tumor-colonized Streptococcus mutans metabolically reprograms tumor microenvironment and promotes oral squamous cell carcinoma – Zhou et al. – Microbiome

Human skin microbiome

Causal relationship between 150 skin microbiomes and prostate cancer: insights from bidirectional mendelian randomization and meta-analysis – Chen et al. – Frontiers in Immunology

Human respiratory microbiome

Microbiome and metabolome patterns after lung transplantation reflect underlying disease and chronic lung allograft dysfunction – Martin et al. – Microbiome

Human gut microbiome

Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia – Gaber et al. – Microbiome

[REVIEW]From gut to bone: deciphering the impact of gut microbiota on osteoporosis pathogenesis and management – Hao et al. – Frontiers in Cellular and Infection Microbiology

[PREPRINT]Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome – Lopez et al. – bioRxiv

[REVIEW]The role of gut microbiota in prostate inflammation and benign prostatic hyperplasia and its therapeutic implications – Chen et al. – Heliyon

Unveiling the gut microbiota blueprint of schizophrenia: a multilevel omics approach – Qi et al. – Frontiers in Psychiatry

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

[PREPRINT]Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis – Gustafson et al. – bioRxiv

Animal microbiome (for animals in the wild)

Gut microbiome in two high-altitude bird populations showed heterogeneity in sex and life stage – Sun et al. – FEMS Microbes

Plant, root, and soil microbiome

Analysis of rhizosphere fungal diversity in lavender at different planting years based on high-throughput sequencing technology – Deng et al. – PLOS One

[PREPRINT]Soil microbiome perturbation impedes growth of Bouteloua curtipendula and increases relative abundance of soil microbial pathogens – Hobbs et al. – bioRxiv

Microbes in space

Adaptation to space conditions of novel bacterial species isolated from the International Space Station revealed by functional gene annotations and comparative genome analysis – Szydlowski et al. – Microbiome

Metabolomics

[PREPRINT]Metabolomics survey of uropathogenic bacteria in human urine – Chan et al. – bioRxiv

Bioinformatics/Resources

[PREPRINT]FungAMR: A comprehensive portrait of antimicrobial resistance mutations in fungi – Bedard et al. – bioRxiv

[PREPRINT]argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO) – Perovic et al. – QUT ePrints

[PREPRINT]BEREN: A bioinformatic tool for recovering Giant viruses, Polinton-like Viruses, and Virophages in metagenomic data – Minch & Moniruzzman – bioRxiv

[DATASET]Dataset of 16S rRNA gene sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan – Ameer et al. – Data in Brief

Techniques

High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform – Lin et al. – PNAS Nexus

October 4, 2024

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Happy Friday! And see you next week at MVIF!

Plastisphere microbiome

What harmful microbes are lurking in the world’s 7 billion tonnes of plastic waste? – Changchao Li – Nature

Respiratory microbiome

Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis – Hongbin Chen – npj Biofilms and Microbiomes

Vaginal microbiome

Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples – Hayden N Brochu – bioRxiv

Oral microbiome

The intensive physical activity causes changes in the composition of gut and oral microbiota – Szymon Urban – Scientific Reports
⚽ “Twenty professional football players and twelve amateurs were invited to the study groups.”

Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome – Yuya Kiguchi – bioRxiv

The association between mode of childbirth delivery and early childhood caries: A comprehensive systematic review and meta-analysis – Li Xiang – PlosOne

Gut microbiome

What’s GABA got to do with it? A potential link between the microbiome, schizophrenia, and the endo-cannabinoid system – Ayala Glinert – Psychiatry Research

Changes in intestinal permeability and gut microbiota following diet-induced weight loss in patients with metabolic dysfunction-associated steatohepatitis and liver fibrosis – Dimitrios A. Koutoukidis – Gut Microbes

Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis – Yan Jia – Scientific Reports

Detailed Analysis of Prebiotic Fructo- and Galacto-Oligosaccharides in the Human Small Intestine – Mara P. H. van Trijp – Journal of Agricultural and Food Chemistry

Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape – Erica T. Grant – Microbiome

Human milk microbiome

Maternal HIV infection and the milk microbiome – Nicole H. Tobin – Microbiome

Viruses and phages

Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens – Mihály Koncz – Cell

Animals

Differential interactions of Rickettsia species with tick microbiota in Rh. sanguineus and Rh. turanicus – Apolline Maitre – Scientific Reports 

Animal experiments

Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer – Rachel C. Fellows – Science Advances

Photoperiod effects on corticosterone and seasonal clocks in cafeteria-induced obese fischer 344 rats are influenced by gut microbiota – Verónica Arreaza-Gil – Scientific Reports 

Plant, root, soil microbiome

Closing the gap: examining the impact of source habitat proximity on plant and soil microbial communities in post-mining spoil heap succession – Lenka Mészárošová – Frontiers in Microbiology

Bacterial Communities from the Antique Roman City of Carnuntum (Austria):16S r-RNA-Based Comparison of Soil Samples from Different Archaeological Horizons – Johann Michael Köhler – preprints

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient – Viviana Freire-Zapata – Nature Microbiology

Phosphorus availability influences disease-suppressive soil microbiome through plant-microbe interactions – Yifan Cao – Microbiome

Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils – Luiz A. Domeignoz-Horta – Nature Communications

Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest – Madison Goforth – Plos One

Drinking water microbiome

Making waves: From tap to gut- exploring the impact of drinking water on gut microbiota – Hanieh Shakeri Moghaddam – Water Research

Bioinformatics

Taxometer: Improving taxonomic classification of metagenomics contigs – Svetlana Kutuzova – Nature Communications

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences – Yasas Wijesekara – bioRxiv

Emergent ecological patterns and modelling of gut microbiomes in health and in disease – Jacopo Pasqualini – Plos Computational Biology

Technique

Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing – Harry T. Child – Access Microbiology

Microbial community interactions on a chip – Duane S. Juang – PNAS

September 19, 2024

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Pregnancy and early life

Networks of human milk microbiota are associated with host genomics, childhood asthma, and allergic sensitization – Fang et al. – Cell Host & Microbe

Affective symptoms in pregnancy are associated with the vaginal microbiome – Scheible et al. – Journal of Affective Disorders

Human oral microbiome

[PREPRINT]An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research – Standeven et al. – bioRxiv

Human gut microbiome

[EDITORIAL]The global epidemic of early-onset cancer: Nature, nurture, or both? – Ogino & Ugai – Annals of Oncology

Akkermania muciniphila: a rising star in tumor immunology – Wang & Tang – Clinical and Translational Oncology

[REVIEW]Nutraceuticals and pharmacological to balance the transitional microbiome to extend immunity during COVID-19 and other viral infections – Kaushal –

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

The role of intestinal microbiota in physiologic and body compositional changes that accompany CLA-mediated weight loss in obese mice – Zhang et al. – Molecular Metabolism

Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice – Masson et al. – Brain, Behaviour, and Immunity

Succession of rumen microbiota and metabolites across different reproductive periods in different sheep breeds and their impact on the growth and development of offspring lambs – Sha et al. – Microbiome

Animal microbiome (for animals in the wild)

[PREPRINT]Microbiome and climate: Skin microbial diversity and community functions of Polypedates megacephalus (Anura: Rhacophoridae) associated with bioclimate – Meegaskumbura et al. – bioRxiv

Plant, root, and soil microbiome

Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles – Wang et al. – Microbiome

Food microbiology

Making yogurt with the ant holobiont uncovers bacteria, acids, and enzymes for food fermentation – Sinotte et al. – bioRxiv

Phages and viruses

Birth of protein folds and functions in the virome – Nomburg et al. – Nature

Bioinformatics

[PREPRINT]An efficient pipeline for creating metagenomic-assembled genomes from ancient oral microbiomes – Standeven et al. – bioRxiv

September 13, 2024

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Happy Friday!
And, see you next week at the MVIF and African Microbiome Day events!

Human microbiome

Gut Microbiome

Transient colonizing microbes promote gut dysbiosis and functional impairment – Sunjae Lee – npj Biofilms and Microbiomes

Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome – Laura Wosinska – Microbiome Research Reports

Gut microbiome and schizophrenia: insights from two-sample Mendelian randomization – Keer Zhou – Schizophrenia

Disease-associated microbiome signature species in the gut – Junhui Li – PNAS Nexus

Nasal microbiome

E-Cigarette Use, Cigarette Smoking, and Sex Are Associated With Nasal Microbiome Dysbiosis Get access Arrow – Elise Hickman – Nicotine & Tobacco Research

Urinary microbiome

Review: Synthesis of current pediatric urinary microbiome research – Layla M. Jeries – Frontiers in Pediatrics

Skin microbiome

The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival – Philipp Licht – npj Biofilms and Microbiomes

Animal microbiome

Antibiotics damage the colonic mucus barrier in a microbiota-independent manner – Jasmin Sawaed – Science Advances

Host diet drives gut microbiome convergence between coral reef fishes and mammals – Samuel Degregori – Molecular Ecology

Functional insights into the effect of feralisation on the gut microbiota of cats worldwide – Ostaizka Aizpurua – bioRxiv

Animal experiments

Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury – Adam M. Hamilton – npj Biofilms and Microbiomes

Ketogenic interventions restore cognition and modulate peripheral metabolic dysfunctions in Alzheimer’s disease mouse models – Paule E. H. M’Bra – bioRxiv

Plant microbiome

The influence of plant traits on soil microbial communities varies between arid and mesic grasslands – Eleonora Egidi – Plant and Soil

Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles – Haitao Wang – Microbiome

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes – F. Fracchia – Microbiome

Built environment

Predicting how varying moisture conditions impact the microbiome of dust collected from the International Space Station – Nicholas Nastasi – Microbiom

The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches – Kenneth Wasmund – Environmental Microbiology

Bioinformatics

Microbial network inference for longitudinal microbiome studies with LUPINE – Saritha Kodikara, Kim-Anh Le Cao – bioRxiv

September 12, 2024

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General microbiome

[REVIEW]Emerging roles of intratumor microbiota in cancer: tumorigenesis and management strategies – Shi, Li & Zhang – Journal of Translational Medicine

[REVIEW]Fungal effectors: past, present, and future – Li et al. – Current Opinion in Microbiology

[Voices]Microbes and metabolites in immunity – Elinav et al. – Immunity

Pregnancy and early life

Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome – Johnson et al. – Cell Genomics

Human urinary tract microbiome

[REVIEW]Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics – Timm, Russell & Hultgren

Human gut microbiome

Dietary-timing-induced gut microbiota diurnal oscillations modulate inflammatory rhythms in rheumatoid arthritis – Ma et al. – Cell Metabolism

Animal microbiome

[PREPRINT]The holobiont’s extracellular microbiome modulates the adaptation of an intracellular endosymbiont – Imchen et al. – bioRxiv

[PREPRINT]Functional insights into the effect of feralisation on the gut microbiota of cats worldwide – Aizpurua et al. – bioRxiv

Microbial community profiling in intestinal tract of indigenous chickens from different villages – Mootane et al. – Scientific Reports

Vitamin B12 ameliorates gut epithelial injury via modulating the HIF-1 pathway and gut microbiota – Feng et al. – Cellular and Molecular Life Sciences

[PREPRINT]Symbiont loss and gain, rather than co-diversification shapes honeybee gut microbiota diversity and function – Prasad et al. – bioRxiv

[PREPRINT]Effects of parental care on skin microbial community composition in poison frogs – Fischer et al. – bioRxiv

Plant, root, and soil microbiome

Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot – Wang et al. – Microbiome

[REVIEW]Re-Envisioning the Plant Disease Triangle: Full Integration of the Host Microbiota and a Focal Pivot to Health Outcomes – Leveau – Annual Review of Phytopathology

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Global marine microbial diversity and its potential in bioprospecting – Chen et al. – Nature

Bioinformatics

Stable biomarker discovery in multi-omics data via canonical correlation analysis – Pusa & Rousu – PLOS One

Techniques

Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples – Li et al. – Microbiome

August 28, 2024

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Human gut microbiome

[REVIEW] Feeding gut microbes to nourish the brain: unravelling the diet–microbiota–gut–brain axis – Elizabeth Schneider et al – Nature Metabolism

Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes – Jordy Evan Sulaiman et al – Nature Communications

Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients – Anna K. Hartikainen et al – NPJ Biofilms & Microbiomes

Impact of probiotics on gut microbiome of extremely preterm or extremely low birthweight infants – Lauren C. Beck et al – Nature Pediatric Research

Effect of Helicobacter pylori on sleeve gastrectomy and gastric microbiome differences in patients with obesity and diabetes – Yong Suk Park et al – International Journal of Obesity

Mining human microbiomes reveals an untapped source of peptide antibiotics – Marcelo D.T. Torres et al – Cell

Both pathogen and host dynamically adapt pH responses along the intestinal tract during enteric bacterial infection – Sarah E. Woodward et al – PLOS Biology

Examination of sex-specific interactions between gut microbiota and host metabolism after 12-week combined polyphenol supplementation in individuals with overweight or obesity – Kelly M. Jardon et al – Gut Microbes

Human vaginal microbiome

The potential of residual clinical Group B Streptococcus swabs for assessing the vaginorectal microbiome in late pregnancy – Laura K. Boelsen et al – Scientific Reports

Animal models

Sex-dependent effects of a high fat diet on metabolic disorders, intestinal barrier function and gut microbiota in mouse – Candice Lefebvre et al – Scientific Reports

Animal microbiome

16S rRNA metabarcoding for the identification of tick-borne bacteria in ticks in the Republic of Korea – Badriah Alkathiri et al – Scientific Reports

The bacterial microbiome and resistome of house dust mites in Irish homes – Amal Aljohani et al – Scientific Reports

Social environment influences microbiota and potentially pathogenic bacterial communities on the skin of developing birds – Ester Martínez-Renau – BMC Animal Microbiome

16S amplicon-based microbiome biomapping of a commercial broiler hatchery – Michael J. Rothrock Jr. et al – BMC Animal Microbiome

Phages & viruses

[REVIEW] Renewed insights into Ackermannviridae phage biology and applications – Anders Nørgaard Sørensen & Lone Brøndsted – NPJ Viruses

Adaptation strategies of giant viruses to low-temperature marine ecosystems – Marianne Buscaglia et al – ISME Journal

Targeted viromes and total metagenomes capture distinct components of bee gut phage communities – Dino Lorenzo Sbardellati et al – BMC Microbiome

Plant, root & soil microbiome

Soil health is associated with higher primary productivity across Europe – Ferran Romero et al – Nature Ecology & Evolution

Pathogen-driven Pseudomonas reshaped the phyllosphere microbiome in combination with Pseudostellaria heterophylla foliar disease resistance via the release of volatile organic compounds – Qing-Song Yuan et al – BMC Environmental Microbiome

Water & extremophile microbiome

Impact of temperature and water source on drinking water microbiome during distribution in a pilot-scale study – Fien Waegenaar et al – NPJ Clean Water

Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa – Anthony M. Smith et al – PLOS One

Nitrite-oxidizing bacteria adapted to low oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones – Samantha G Fortin et al – ISME Journal

Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments – Chyrene Moncada et al – ISME Journal

Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica – Hanbyul Lee et al – BMC Environmental Microbiome

Tools & methods

Intestinal organ chips for disease modelling and personalized medicine – Alican Özkan et al – Nature Reviews Gastroenterology & Hepatology

MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using Machine lEarning Techniques – Edoardo Bizzotto et al – BMC Environmental Microbiome

refMLST: reference-based multilocus sequence typing enables universal bacterial typing – Mondher Khdhiri et al – BMC Bioinformatics

Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization – Weixian Liu et al – BMC Bioinformatics