Category Archives: Water microbiome

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 24, 2024

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Human microbiome

Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease – Xiangge Tian et al – BMC Microbiome

The Role of Gut Microbiota in the Neuroprotective Effects of Selenium in Alzheimer’s Disease – Anatoly V. Skalny et al – Molecular Neurobiology

[REVIEW] The oral–gut microbiome axis in health and disease – Benoit J. Kunath – Nature Reviews Microbiology

Enhancing gut microbiota and microbial function with inulin supplementation in children with obesity – Chonnikant Visuthranukul et al – International Journal of Obesity

Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder – Zaiquan Dong et al – Journal of Affective Disorders

Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health – Na Han et al – Frontiers in Microbiology

Skin locations inference and body fluid identification from skin microbial patterns for forensic applications – Litao Huang et al – Forensic Science International

Animal experiments

Improving insulin resistance by sulforaphane via activating the Bacteroides and Lactobacillus SCFAs–GPR–GLP1 signal axis – Sicong Tian et al – Food & Function

Gastroprotective and microbiome-modulating effects of ubiquinol in rats with radiation-induced enteropathy – Walaa A. Eraqi et al – BMC Animal Microbiome

Animal microbiome

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses – Mason R. Stothart et al – Nature Communications

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale – Shuai Du et al – Environmental Science & Technology

Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages – Marwa Mamdouh Tawfik et al – BMC Animal Microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Laura Glendinning et al – BMC Microbiome

Water & extremophile microbiome

Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton – Tianyi Chang et al – BMC Microbiome

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake – Arianna I. Krinos et al – BMC Microbiome

Built environment microbiome

[PREPRINT] Utilizing the biosimulator to analyze the environmental microbiome within the intensive care units of a hospital – Sunil Thomas et al – ResearchSquare

Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system – Dou Wang et al – BMC Microbiome

Plant, root, & soil microbiome

Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China – Jie-Liang Liang et al – BMC Microbiome

Bioinformatics tools

MIDASim: a fast and simple simulator for realistic microbiome data – Mengyu He et al – BMC Microbiome

June 26, 2024

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Human gut microbiome

Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut – Nick Quinn-Bohmann et al – Nature Microbiology

Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes – Katherine Ramos Sarmiento et al – ISME Journal

Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota – Anurag K. Sinha – Nature Microbiology

Animal models

The zebrafish gut microbiome influences benzo[a]pyrene developmental neurobehavioral toxicity – Keaton Stagaman et al – Nature Scientific Reports

Modulation of gut microbiota composition due to early weaning stress induces depressive behavior during the juvenile period in mice – Itsuka Kamimura et al – BMC Animal Microbiome

Antibiotics affect the pharmacokinetics of n-butylphthalide in vivo by altering the intestinal microbiota – Xiangchen Li et al – PLOS One

Trilobatin ameliorates dextran sulfate sodium-induced ulcerative colitis in mice via the NF-κB pathway and alterations in gut microbiota – Nanbo Wang et al – PLOS One

Animal microbiome

Gut microbiota and immune profiling of microbiota-humanised versus wildtype mouse models of hepatointestinal schistosomiasis – K.A. Stark et al – BMC Animal Microbiome

Analysis of differences in the rumen microbiome and metabolic function in prepartum dairy cows with different body condition scores – Dewei Du et al – BMC Animal Microbiome

Improvement of insulin sensitivity by dietary fiber consumption during late pregnant sows is associated with gut microbiota regulation of tryptophan metabolism – Yang Li – BMC Animal Microbiome

Gut microbiota diversity in a dung beetle (Catharsius molossus) across geographical variations and brood ball-mediated microbial transmission – Hao-Yu Chen et al – PLOS One

Water & extremophile microbiomes

Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent – Rui Liu – BMC Environmental Microbiome

Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary – Ziheng Wu et al – BMC Microbiome

Plant, root, & soil microbiome

Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders – Jibing Li – ISME Journal

Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments – Shasha Wang et al – ISME Journal

Other microbes

Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates – Qi Song et al – ISME Journal

Bioinformatics & tools

Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling – Worakorn Phumiphanjarphak & Pakorn Aiewsakun – BMC Bioinformatics

Methods

Soft autonomous ingestible device for sampling the small-intestinal microbiome – Ruben Del-Rio-Ruiz et al – Cell Device

June 19, 2024

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Oral and respiratory microbiota

Safety, Feasibility, and Advantages of Oral Microbiota Transplantation: The First Clinical Case – Oleg V. Goloschapov – Journal of Pediatric Hematology/Oncology

Oral microbial dysbiosis in patients with oral cavity cancers – Ozge Unlu – Clinical Oral Investigations

Nasal cathelicidin is expressed in early life and is increased during mild, but not severe respiratory syncytial virus infection – Sofia Sintoris – Nature Scientific Reports

Human gut microbiome

Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges – Lucas Masier – Nature Metabolism

Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice – Yohannes Seyoum – Nature Communications

Beneficial microbes and compounds

Short-chain fatty acid valerate reduces voluntary alcohol intake in male mice – Suresh C. Bokoliya – BMC Microbiome

Sleep promoting and omics exploration on probiotics fermented Gastrodia elata Blume – Chao-Qi Zhang – NPJ Science of Food

Animal microbiome

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human – Li Tian – BMC Microbiome

Water and extremophile microbiome

Bacterial community and cyanotoxin gene distribution of the Winam Gulf, Lake Victoria, Kenya – Katelyn M. Brown – Environmental Microbiology

Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water – Nataliya Teteneva – ISME Journal

Plant, root, and soil microbiomes

Root-associated Streptomyces produce galbonolides to modulate plant immunity and promote rhizosphere colonization – Clément Nicolle – ISME Journal

Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome – Zi-Teng Liu – Nature Communications

Conceptualizing soil fauna effects on labile and stabilized soil organic matter – Gerrit Angst – Nature Communications

Fungi

The first ITS1 profiling of honey samples from the Southeast Asian region Lombok, Bali and Banggi Island – Saeed Ullah – Nature Scientific Reports

Archaea

Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery – Biyan Huang – ISME Journal

Microbial Ecology

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution – Hagay Enav – Nature Biotechnology

Methods

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding – Karl D. Gaisser – Nature Protocols

Commentary and opinions

SeqCode in the golden age of prokaryotic systematics – Diego Javier Jiménez – ISME Journal

Digestive Disease Week 2024 – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Barriers and enablers to the effective implementation of omics research in low- and middle-income countries – Jacus S. Nacis – Nature Biotechnology

June 12, 2024

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Human gut microbiome

Persistence and Sexual Dimorphism of Gut Dysbiosis and Pathobiome after Sepsis and Trauma – Jennifer A. Munley – Annals of Surgery

[REVIEW] COVID-19 influenced gut dysbiosis, post-acute sequelae, immune regulation, and therapeutic regimens – Sterlin T. Raj – Frontiers in Cellular and Infection Microbiology

Novel probiotic preparation with in vivo gluten-degrading activity and potential modulatory effects on the gut microbiota – Olga Nikoloudaki – Microbiology Spectrum

Adaptation to tolerate high doses of arabinoxylan is associated with fecal levels of Bifidobacterium longum – Edward C. Deehan – Gut Microbes

Vaginal microbiome

Co-evolution of vaginal microbiome and cervical cancer – Menglu Hu – BMC Journal of Translational Medicine

Animal experiments

Establishment of a novel obesity mouse model: the induction of intestinal microbiota dysbiosis – Qiuju Li – Scientific Reports

Bacteroides uniformis CECT 7771 requires adaptive immunity to improve glucose tolerance but not to prevent body weight gain in diet-induced obese mice – Marina Romaní-Pérez – BMC MIcrobiome

Animal microbiome

Oral microbiome sequencing revealed the enrichment of Fusobacterium sp., Porphyromonas sp., Campylobacter sp., and Neisseria sp. on the oral malignant fibroma surface of giant panda – Xiaowan Wang – Frontiers in Microbiology

Effect of microplastics pollution on the gut microbiome of anecic and endogeic earthworms – Christina Papazlatani – FEMS Microbiology Letters

Evolutionary history of tyrosine-supplementing endosymbionts in pollen-feeding beetles – Jürgen C Wierz – ISME Journal

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization – Ke Zhang – BMC MIcrobiome

Plant, root, and soil microbiome

Fungal biomass and ectomycorrhizal community assessment of phosphorus responsive Pinus taeda plantations – Jacob Hackman – Frontiers in Fungal Biology

Soil conditioner improves soil properties, regulates microbial communities, and increases yield and quality of Uncaria rhynchophylla – Qian Liu – Scientific Reports

Genetic control of rhizosphere microbiome of the cotton plants under field conditions – Feng Wei – Applied Microbiology and Biotechnology

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost – Yaoming Li – mSphere

Sewage Sludge Promotes the Accumulation of Antibiotic Resistance Genes in Tomato Xylem – Wen-Jing Li – Environmental Science and Technology

Water and extremophile microbiome

Plastic and terrestrial organic matter degradation by the humic lake microbiome continues throughout the seasons – Jussi S. Vesamäki – Environmental Microbiology Reports

Coral microbiomes are structured by environmental gradients in deep waters – Samuel A. Vohsen – BMC Environmental Microbiome

June 7, 2024

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Today’s digest features AMPSphere, Candida pathogenesis, rhizosphere microbiome in the Himalayas, imaging of oral microbiome, and more.
See you at #MVIF special event on women’s health!

Global microbiome

Discovery of antimicrobial peptides in the global microbiome with machine learning – Célio Dias Santos-Júnior and Marcelo D.T. Torres – Cell

Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes – Craig Liddicoat – Science of The Total Environment

Infant microbiome

The impact of perinatal maternal stress on the maternal and infant gut and human milk microbiomes: A scoping review protocol – Niamh Ryan – Plos One

Oral microbiome

Improved Visualization of Oral Microbial Consortia – S.T. Ramirez-Puebla – Journal of Dental Research

Animal microbiome

Changes of faecal bacterial communities and microbial fibrolytic activity in horses aged from 6 to 30 years old – Marylou Baraille – Plos One

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization – Ke Zhang – Microbiome

Animal experiments

Bacteroides uniformis CECT 7771 requires adaptive immunity to improve glucose tolerance but not to prevent body weight gain in diet-induced obese mice – Marina Romaní-Pérez – Microbiome

The impact of microplastics polystyrene on the microscopic structure of mouse intestine, tight junction genes and gut microbiota – Qi-Ling Su – Plos One

Epithelial hypoxia maintains colonization resistance against Candida albicans – Hannah P. Savage – Cell Host & Microbe

Viruses and phages

Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs – Jun Hu – Microbiome

Water microbiome

Deep long-read metagenomic sequencing reveals niche differentiation in carbon cycling potential between benthic and planktonic microbial populations – Tomeu Viver – bioRxiv

Root, soil, plant microbiome

Altitude-Dependent Influence of Artemisia brevifolia on its Rhizosphere Microbiome in Ladakh Region of the Western Himalayas – Manzoor Hussain – Rhizosphere

Bioinformatics

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet – Nicolae Sapoval – bioRxiv

Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion – Xiaofan Jin – bioRxiv

June 5, 2024

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Human gut microbiome

Gut microbiome and inflammation among athletes in wheelchair in a crossover randomized pilot trial of probiotic and prebiotic interventions – Ezra Valido – Nature Scientific Reports

A microbiota-directed complementary food intervention in 12-18-month-old Bangladeshi children improves linear growth – Ishita Mostafa – eBioMedicine

Gut microbiome shifts in people with type 1 diabetes are associated with glycaemic control: an INNODIA study – Tommi Vatanen – Diabetologia

Association of methyl donor nutrients dietary intake and sleep disorders in the elderly revealed by the intestinal microbiome – Qianqian Chen – Food & Function

[REVIEW] The human gut microbiome and aging – Evan Bradley & John Haran – Gut Microbes

[REVIEW] Nurturing gut health: role of m6A RNA methylation in upholding the intestinal barrier – Shuaijie Wang – Cell Death Discovery

Persistent dysbiosis of duodenal microbiota in patients with controlled pediatric Crohn’s disease after resolution of inflammation – Rebecca Pierce – Nature Scientific Reports

Dysfunctional circadian clock accelerates cancer metastasis by intestinal microbiota triggering accumulation of myeloid-derived suppressor cells – Jing-Lin Liu – Cell Metabolism

Human respiratory microbiome

Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure – Georgios D. Kitsios – Nature Communications

Lack of correlation between in vitro and within patient measures of P. aeruginosa biofilms in cystic fibrosis – Amanda J Morris – Cell Heliyon

Human oral microbiome

The oral microbiome and oral and upper gastrointestinal diseases – Sifan Liu – Journal of Oral Microbiology

Comprehensive analysis of the oral microbiota and metabolome change in patients of burning mouth syndrome with psychiatric symptoms – Shihong Luo – Journal of Oral Microbiology

Candida albicans natural diversity: a resource to dissect fungal commensalism and pathogenesis – Elena Lindemann-Perez – Current Opinion in Microbiology

Animal experiments

Prevotella copri transplantation promotes neurorehabilitation in a mouse model of traumatic brain injury – Nina Gu – Journal of Neuroinflammation

Spatial recovery of the murine gut microbiota after antibiotics perturbation – M. Taguer – mBio

Water and extremophile microbiome

Global biogeography of microbes driving ocean ecological status under climate change – Zhenyan Zhang – Nature Communications

Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens – Natalia Timanikova – Environmental Microbiology

Viruses & phages

Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study – Jean-Paul Pirnay – Nature Microbiology

Built environment microbiome

Environmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border – Lauren D. Benton – Nature Scientific Reports

Plant, root and soil microbiome

Tibetan Plateau grasslands might increase sequestration of microbial necromass carbon under future warming – Qinwei Zhang – Nature Communications Biology

Assembly of Endophytic Communities of Setaria viridis Plants when Grown in Different Soils and Derived from Different Seeds – Carolina Escobar Rodríguez – Phytobiomes

[PREPRINT] Hybrid xyloglucan utilisation loci are prevalent among plant-associated Bacteroidota – Hannah Martin – bioRxiv

Microbial ecology

Cooperative growth in microbial communities is a driver of multistability – William Lopes – Nature Communications

Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes – Craig Liddicoat – Science of the Total Environment

Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure – Paul Oladele – Microbiology Spectrum

May 29, 2024

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Human microbiomes

Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction – Alex E. Mohr – Nature Communications

[PREPRINT] Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome – Abishek Goel – bioRxiv

Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome – Francesca De Fillipis – Nature Communications

The interrelation between microbial immunoglobulin coating, vaginal microbiota, ethnicity, and preterm birth – H.J. Schuster – BMC Microbiome

Porphyromonas gingivalis, a bridge between oral health and immune evasion in gastric cancer – Matías Muñoz-Medel – Frontiers in Oncology

Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study – Jung Soo Park – Journal of Periodontal Resaerch

Animal microbiome

Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis – S. Casaro – BMC Animal Microbiome

Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes – Shichun He – BMC Microbiology

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis – Yujie Meng – BMC Microbiome

Co-habiting ants and silverfish display a converging feeding ecology – Thomas Parmentier – BMC Biology

Temperature-dependent differences in mouse gut motility are mediated by stress – Alvin Han – Nature Lab Animal

Food microbiome

Evaluation of microbiota-induced changes in biochemical, sensory properties and volatile profile of kombucha produced by reformed microbial community – Hilal Kilmanoglu – Food Chemistry X

Plant, soil, and root microbiome

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle – Bridget B. McGivern – Nature Microbiology

[PREPRINT] Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils – Samuel E. Barnett & Ashley Shade – bioRxiv

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome – Yoko Masuda – BMC Microbiome

Water & extremophile microbiome

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution – Brune Jounnard & Concepcion Sanchez-Cid – BMC Microbiome

Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron – Biao Yu – Frontiers in Microbiology

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria – Subhash Yadav – BMC Microbiome