Category Archives: Animal experiments

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

August 14, 2024

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Human microbiome

Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs – Eugeni Belda et al – BMC Medical Genomics

The impact of breastfeeding on the preterm infant’s microbiome and metabolome: a pilot study – Keriann Schulkers Escalante et al – Nature Pediatric Research

[REVIEW] The human microbiome in space: parallels between Earth-based dysbiosis, implications for long-duration spaceflight, and possible mitigation strategies – Sofia Etlin et al – Clinical Microbiology Reviews

MASS cohort: Multicenter, longitudinal, and prospective study of the role of microbiome in severe pneumonia and host susceptibility – Xin Wei et al – iMeta

Distinctive duodenal microbiomes and bile acid profiles in duodenal tumor patients revealed by prospective observational study – Yoko Kubosawa et al – Nature Scientific Reports

Elucidating the dynamics and impact of the gut microbiome on maternal nutritional status during pregnancy, effect on pregnancy outcomes and infant health in rural Pakistan: study protocol for a prospective, longitudinal observational study – Yaqub Wassan et al – BMJ Open

Time-varying ambient air pollution exposure is associated with gut microbiome variation in the first 2 years of life – Tianlai Qiu et al – Environmental Pollution

Animal experiments

Gut Microbiota-Induced Modulation of the Central Nervous System Function in Parkinson’s Disease Through the Gut-Brain Axis and Short-Chain Fatty Acids – Yiting Ni et al – Molecular Neurobiology

Animal microbiome

Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria – Junbo Tang et al – Nature Communications

Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata – Gagandeep Brar et al – Applied & Environmental Microbiology

Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition – Lingyan Ma & Wentao Lyu et al – iMeta

Meconium microbiota in naturally delivered canine puppies – Alessia Bertero et al – BMC Veterinary Research

Gut microbiome perturbation and its correlation with tylosin pharmacokinetics in healthy and infected pigs – Eon-Bee Lee et al – Nature Scientific Reports

Beneficial microbes, compounds, & foods

Restriction of growth and biofilm formation of ESKAPE pathogens by caprine gut-derived probiotic bacteria – Prerna Saini et al – Frontiers in Microbiology

[REVIEW] Polyphenols improve non-alcoholic fatty liver disease via gut microbiota: A comprehensive review – Kimia Mohammadhasani et al – Food Science & Nutrition

[REVIEW] Exploring the Potential of Postbiotics for Food Safety and Human Health Improvement – Folayemi Janet Isaac-Bamgboye et al – Journal of Nutrition & Metabolism

Transcriptomics and gut microbiome analysis of the edible herb Bidens pilosa as a functional feed additive to promote growth and metabolism in tilapia (Oreochromis spp.) – Che-Chun Chen et al – BMC Genomics

[REVIEW] A comprehensive review of the characterization, host interactions, and stabilization advancements on probiotics: Addressing the challenges in functional food diversification – Eskindir Getachew Fentie et al – Comp. Rev. in Food Science & Safety

Effects of kefir consumption on gut microbiota and health outcomes in women with polycystic ovary syndrome – Merve Esra Çıtar Dazıroğlu – Food Science & Nutrition

Plant, root, & soil microbiome

Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species – Anastasiia Fetsiukh et al – Nature Scientific Reports

Differences in the constituents of bacterial microbiota of soils collected from two fields of diverse potato blackleg and soft rot diseases incidences, a case study – Weronika Babinska-Wensierska et al – Nature Scientific Reports

Variations of soil metal content, soil enzyme activity and soil bacterial community in Rhododendron delavayi natural shrub forest at different elevations – Li Wang et al – BMC Microbiology

Effective microorganism combinations improve the quality of compost-bedded pack products in heifer barns: exploring pack bacteria-fungi interaction mechanisms – Zhenbin Zhang et al – BMC Microbiology

Global patterns in the growth potential of soil bacterial communities – Ernest D. Osburn et al – Nature Communications

Microplastic-contamination can reshape plant community by affecting soil properties – Mengzuan He et al – Ecotoxicology & Environmental Safety

Water & extremophile microbiome

Microbial Succession on Microplastics in Wastewater Treatment Plants: Exploring the Complexities of Microplastic-Microbiome Interactions – Klaudia Kwiatkowska & Paulina Ormaniec – Microbial Ecology

Microbial ecology

Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology – Oscar Gallardo-Navarro et a – Heliyon

Antibiotic resistance

[NEWS FEATURE] Five ways science is tackling the antibiotic resistance crisis – Amber Dance – Nature

Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life – Pål Trosvik et al – Nature Scientific Reports

Bioinformatics tools

MetaBakery: a Singularity implementation of bioBakery tools as a skeleton application for efficient HPC deconvolution of microbiome metagenomic sequencing data to machine learning ready information – Boštjan Murovec et al – Frontiers in Microbiology

August 8, 2024

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Human respiratory, skin, and gut microbiome

Nurturing futures through the maternal microbiome – Roberta Pala & Katherine Kenny – Sociology of Health & Illness

The skin microbiota of preterm infants and impact of diaper change frequency – Noelle E. Younge et al – PLOS One

Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity – Ana M. Valdes et al – BMC Medicine

Gut microbial composition is altered in sarcopenia: A systematic review and meta-analysis of clinical studies – Xiaohong Mai et al – PLOS One

Associations of upper respiratory mucosa microbiota with Rheumatoid arthritis, autoantibodies, and disease activity – Young Bin Joo et al – PLOS One

Effect of β-lactam antibiotics on the gut microbiota of term neonates – Hongdan Gu et al – BMC Annals of Clinical Microbiology & Antimicrobials

Clinical efficacy of a multilamellar cream on skin physiology and microbiome in an epidermal stress model: A controlled double-blinded study – Joachim W Fluhr et al – Int. Journal of Cosmetic Science

Animal experiments

Mouse adaptation of human inflammatory bowel diseases microbiota enhances colonization efficiency and alters microbiome aggressiveness depending on the recipient colonic inflammatory environment – Simon M. Gray et al – BMC Microbiome

Animal microbiome

Gut microbiota composition of the isopod Ligia in South Korea exposed to expanded polystyrene pollution – Young-Mi Lee et al – PLOS One

Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome – Patrizia Robino et al – BMC Biological Research

Survey of antimicrobial and probiotic use practices in wildlife rehabilitation in the United States – Elizabeth A. Miller et al – PLOS One

The impact of management on the fecal microbiome of endangered greater sage-grouse (Centrocercus urophasianus) in a zoo-based conservation program – Emma Vaasjo et al – Conservation Physiology

Water & extremophile microbiome

Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome – Pablo Suárez-Moo et al – Environmental Microbiology

Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column – Su Ding et al – ISME Journal

Plant, root & soil microbiome

Characterization of fungal microbiome structure in leaf litter compost through metagenomic profiling for harnessing the bio-organic fertilizer potential – Sophayo Mahongnao et al – 3Biotech

Plant species influences the composition of root system microbiome and its antibiotic resistance profile in a constructed wetland receiving primary treated wastewater – Valentina Riva et al – Frontiers in Microbiology

DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories – Esteban E. Nieto et al – BMC Microbiome

Seed endophytes and rhizosphere microbiome of Imperata cylindrica, a pioneer plant of abandoned mine lands – Wenqin Mao et al – Frontiers in Microbiology

Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients – Xing Huang et al – ISME Journal.

Microbial ecology

[PREPRINT] Models of microbiome evolution incorporating host resource provisioning – Yao Xiao et al – bioRxiv

Beneficial microbes & compounds

Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo – Florac De Bruyn et al – Nature Communications Biology

August 01, 2024

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Pregnancy and early life

Diet at birth is critical for healthy growth, independent of effects on the gut microbiota – van den Elsen et al. – Microbiome

Human oral microbiome

Comparative analysis of microbiome in coronal and root caries – Gondo et al. – BMC Oral Health

Human gut microbiome

Gut microbiota carcinogen metabolism causes distal tissue tumours – Roje et al. – Nature

Time-Dependent Shifts in Intestinal Bacteriome, Klebsiella Colonization and Incidence of Antibiotic-Resistance Genes after Allogeneic Hematopoietic Stem Cell Transplantation – Moiseev et al. – biomedicines

[PREPRINT]Comparative analysis of the treatment-naive microbiome across rheumatic diseases to predict MTX treatment response – Amend et al. – bioRxiv

Meta-analysis identifies common gut microbiota associated with multiple sclerosis – Lin et al. – Genome Medicine

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

[PREPRINT]Ganoderma lucidum alleviates kidney aging by modulating gut microbiota – Liu et al. – bioRxiv

[PREPRINT]Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice – Ozcan et al. – bioRxiv

Effects of antibiotic cocktail on the fecal microbiota and their potential correlation of local immune response – Liu et al. – BMC Microbiology

Plant, root, and soil microbiome

[REVIEW]Practical applications of soil microbiota to improve ecosystem restoration: current knowledge and future directions – Peddle et al. – Biological Reviews

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

Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes – Roager et al. – mSystems

Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean – Zhao et al. – Nature Communications

Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea – Kolenc et al. – Science of The Total Environment

Built environment (subways, indoor surfaces)

A global metagenomic map of urban microbiomes and antimicrobial resistance – Danko et al. – Cell

Bioinformatics

Solving genomic puzzles: computational methods for metagenomic binning – Mallawaarachchi et al. – Briefings in Bioinformatics

July 31, 2024

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Human gut microbiome

The gut mycobiome signatures in long-lived populations – Lixia Pu et al – Cell iScience

Viral metagenomics combined with non-targeted serum metabolomics reveals the role of enteroviruses in a mouse model of coronary heart disease – Xiang Li et al – BMC Virology

Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria – Ting Zhang et al – ISME Journal

Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota – David Bars-Cortina et al – BMC Genomics

Effect of different delivery modes on intestinal microbiota and immune function of neonates – Chunhui Lai et al – Scientific Reports

Animal experiments

Effects of Akkermansia muciniphila on Gut Morphology, Antioxidant Indices, and Gut Microbiome of Mice Under Heat Stress – Caiyu Luo et al – Foodborne Pathogens and Disease

Gut microbiota mediates the anti-inflammatory effects of supplemental infrared irradiation in mice – Shijing Wang et al – Photochemistry and Photobiology

Short-chain fatty acids ameliorate imiquimod-induced skin thickening and IL-17 levels and alter gut microbiota in mice: a metagenomic association analysis – Yi-Ju Chen et al – Scientific Reports

Animal microbiome

Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus – Masayuki Kaneko et al – ISME Communications

Rodents consuming the same toxic diet harbor a unique functional core microbiome – Tess E. Stapleton et al – BMC Animal Microbiome

The plant-sucking insect selects assembly of the gut microbiota from environment to enhance host reproduction – Hong-Wei Shan et al – NPJ Biofilms and Microbiomes

Alterations in captive Alexandrine parakeet (Palaeornis eupatria) gut microbiome and metabolome in response to dietary change – Xin Feng et al – Comparative Biochemistry and Physiology

Link between bacterial communities and contrasted loads in ectoparasitic monogeneans from the external mucus of two wild sparid species (Teleostei) – Judith Revault et al – BMC Animal Microbiome

Beneficial microbes and compounds

Unearthing Lactococcus lactis and Scheffersomyeces symbionts from edible wood-boring beetle larvae as a bio-resource for industrial applications – Shadrick Kibet et al – BMC Microbiology

Plant, root, and soil microbiome

[OPINION] Microbiome Bioprospecting for Sustainable Agrobiome and Circular Bioeconomy – Dhananjaya Pratap Singh – Anthropocene Science

Host genetic variation and specialized metabolites from wheat leaves enriches for phyllosphere Pseudomonas spp. with enriched antibiotic resistomes – Qian Xiang et al – ISME Journal

Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health – Morgane Duret et al – Microbiological Research

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan – Kohei Hamamoto et al – BMC Environmental Microbiome