Tag Archives: health

November 14, 2025

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Gut Microbiome & Host Health

Sleep deprivation disrupts diurnal rhythmicity of gut microbiota and blood inflammatory cytokines in mice — Weiran Shan et al. (PLOS ONE)

Chemical modulation of gut bacterial metabolism induces colanic acid and extends the lifespan of nematode and mammalian hosts — Guo Hu et al. (PLOS Biology)

The role of hypothyroidism in cirrhosis pathogenesis: A retrospective cohort study and multi-omics integration analysis — Ziyang Yang et al. (PLOS Genetics)

Multi-omics analysis reveals metabolic regulation of phosphatidylcholine, triglycerides, phosphatidylethanolamine, and cardiolipin metabolism in mouse liver with MASLD — Hong Liang & Kang Song (PLOS ONE)

Metabolomics and glucose tolerance in pregnancy and postpartum: The PONCH study — Ulrika Andersson-Hall et al. (PLOS ONE)

Microbial Pathogens, Immunity & Infection

Exploring the gut microbiota of Pacific white shrimp suffering pale shrimp disease — Lalitphan Kitsanayanyong et al. (PLOS ONE)

Dominance of Zygosaccharomyces and shifts in bacterial pathways under antimicrobial pressure — Maria Cecilia Rasuk et al. (PLOS ONE)

How transcriptional networks control Verticillium plant infection — Ying-Yu Chen et al. (PLOS Pathogens)

Integrative machine learning and multi-omics framework identifies shared biomarkers for rheumatoid arthritis and ulcerative colitis — Meili Liu et al. (PLOS ONE)

The cervicovaginal microbiome associates with spatially restricted host transcriptional signatures throughout the ectocervical epithelium — Vilde Kaldhusdal et al. (PLOS Pathogens)

Characterization of ORF19.7608 (PPP1), a biofilm-induced gene of Candida albicans — Nmerichukwu C. Iwuchukwu et al. (PLOS ONE)

Differential regulation of the eicosanoid biosynthesis pathway during Enterocytozoon hepatopenaei infection in shrimp — Wananit Wimuttisuk et al. (PLOS ONE)

Animal, Environmental & Soil Microbiomes

Cuts or carcasses? Diet form affects fecal microbial and fiber fractions in Asiatic lions — Mengmeng Sun et al. (PLOS ONE)

From pre-oral secretions to gut digestion: How Lucilia sericata larvae handle Leishmania major — Azam Malekian et al. (PLOS ONE)

Targeted pathogen profiling of ancient feces reveals common enteric infections (725–920 CE) — Drew Capone et al. (PLOS ONE)

Starve or share? Phosphate availability shapes plant–microbe interactions — Maja Schmidt et al. (PLOS Pathogens)

Pathogenicity and transmission of Morganella morganii in honey bees — Yijun Chen & Qiang Huang (PLOS Pathogens)

Mitogenomics of the tropical bont tick reveals vertical and horizontal transmission of Rickettsia africae — Elisha Chatanga et al. (PLOS NTDs)

Differentiation of bacterial communities in the coral Orbicella faveolata across life-cycle stages — Amanda Pérez-Trejo et al. (PLOS ONE)

Insect-derived polymer hydrogel based on fibroin matrix from whole silkworm larvae — Maki Yamazaki et al. (PLOS ONE)

Thermophilic microbiome acclimation improves anaerobic digestion of food waste — Hengxuan Shao et al. (PLOS ONE)

Epidemiology, Public Health & Clinical Microbiology

Assessing piperacillin/tazobactam vs. ceftriaxone + metronidazole for children with perforated appendicitis — Daniel Briatico et al. (PLOS ONE)

Prevalence and antimicrobial resistance of multidrug-resistant Staphylococcus epidermidis in raw milk — Inamullah et al. (PLOS ONE)

Hematological ratios, immune-related adverse events, and mortality in patients receiving immune checkpoint inhibitors — Sophie Lekkerkerker et al. (PLOS ONE)

Geographical and climatic risk factors for COVID-19 in southwest Iran — Koorosh Nikaein et al. (PLOS ONE)

Anthropometric and neurocognitive consequences of Campylobacter, ETEC, and norovirus infections: A systematic review — Patricia B. Pavlinac et al. (PLOS NTDs)

Neuroscience, Immunology & Molecular Networks

Skin melanin is associated with body temperature regulation in humans and mice — Kale S. Bongers et al. (PLOS ONE)

Oxytocin neurons drive melanocortin circuit maturation via vesicle release — Pierre-Yves Barelle et al. (PLOS Biology)

Elucidation and application of the neuroimmune axis between depression and autoimmune diseases — Fu Sun et al. (PLOS ONE)

Quantifying microbial interactions using an iterative generalized Lotka–Volterra approach — Yue Huang et al. (PLOS Computational Biology)

October 2, 2024

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Gut Microbiome

Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants – Brandon Hickman et al – Nature Communications

Pangenomes of human gut microbiota uncover links between genetic diversity and stress response – Saar Shoer et al – Cell Host & Microbe

[MINI REVIEW] The human gut microbiome in health and disease: time for a new chapter? – Jee-Yon Lee et al – ASM Infection & Immunity

Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities – Amin Valiei et al – NPJ Biofilms & Microbiomes

A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases – Wen Sun et al – NPJ Biofilms & Microbiomes

A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome – Tetsuro Kawano-Sugaya et al – BMC Microbiome

Stratification of human gut microbiomes by succinotype is associated with inflammatory bowel disease status – Laura Anthamatten et al – BMC Microbiome

Impact of complementary feeding on infant gut microbiome, metabolites and early development – Yudong Shi et al – Food & Function

Can longer lifespan be associated with gut microbiota involvement in lipid metabolism? – Sára Šardzíková et al – FEMS Microbiology Ecology

Beneficial microbes & compounds

[REVIEW] Preventive effect of probiotics on oral mucositis induced by anticancer therapy: a systematic review and meta-analysis of randomized controlled trials – Bo Yang et al – BMC Oral Health

Animal Microbiome

Bacteria from the Amycolatopsis genus associated with a toxic bird secrete protective secondary metabolites – Elena Seibel et al – Nature Communications

Impact of virginiamycin on the ruminal microbiota of feedlot cattle – Bruna Parapinski Santos – Canadian Journal of Veterinary Research

Microbiome of death

From carrion to soil: microbial recycling of animal carcasses – Jennifer M. DeBruyn et al – Cell Trends in Microbiology

Water & extremophile microbiome

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

Prescribed fire regimes influence responses of fungal and bacterial communities on new litter substrates in a brackish tidal marsh – Viet Q. Dao et al – PLOS One

Plant, root & soil microbiome

The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota – Anderson O. Oaikhena et al – Scientific Reports

Water‒soil-air‒plant mutual feedback mechanism under the application of red bed composite polymers – Tianpeng Chen et al – PLOS One

Diversity and community distribution of soil bacterial in the Yellow River irrigation area of Ningxia, China – Xia Wu et al – PLOS One

Bioinformatics & tools

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs – Annika Jochheim et al – BMC Microbiome

September 29, 2024

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Human and General Microbiome

Gut microbiota drives colon cancer risk associated with diet: a comparative analysis of meat-based and pesco-vegetarian diets – Carlotta De Filippo – Microbiome

Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics – Georges P Schmartz – Nature Communications

Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness – Minghui Cheng – Nature Communications

Small Bowel Microbiome Profiles in Overweight and Obese Humans – Liqi Li – The American Journal of Gastroenterology

Intratumoral microbiota as a novel prognostic indicator in bladder cancer – Yuwei Zhang – Scientific Reports

Research Highlight: Identifying antimicrobials in the human microbiome – Sarah Crunkhorn – Nature Reviews. Drug Discovery

Review: Akkermansia muciniphila as a Potential Guardian against Oral Health Diseases: A Narrative Review – Molly H Anderson – Nutrients

Review: Intratumoral microbiota in colorectal cancer: focus on specific distribution and potential mechanisms – Jing Long – Cell Communication and Signaling

Review: Bacterial extracellular vesicles at the interface of gut microbiota and immunity – Inês Melo-Marques – Gut Microbes

Beneficial Microbes and Compounds

GV-971 prevents severe acute pancreatitis by remodeling the microbiota-metabolic-immune axis – Xi Chen – Nature Communications

Fecal Microbiota Transplantation-Mediated Rebalancing of the Gut-Brain Axis Alleviates Cisplatin-Induced Neuropathic Pain – Mousmi Rani – ACS Chemical Neuroscience

FMT rescues mice from DSS-induced colitis in a STING-dependent manner – Dan Pu – Gut Microbes

Aged garlic oligosaccharides modulate host metabolism and gut microbiota to alleviate high-fat and high-cholesterol diet-induced atherosclerosis in ApoE(-/-) mice – Xiaomin Wang – Food Chemistry

Phytoactives for Obesity Management: Integrating Nanomedicine for Its Effective Delivery – Ashok Kumar Mandal – Nutrition Reviews

Animal Microbiome

Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes – Georges P Schmartz – Nature Communications

Fur microbiome as a putative source of symbiotic bacteria in sucking lice – Jana Martin Říhová – Scientific Reports

Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice – Feiling Huang – BMC Microbiology

Dietary fiber intake impacts gut bacterial and viral populations in a hypertensive mouse model – Laura Avellaneda-Franco – Gut Microbes

Effect of shipping on the microbiome of donor mice used to reconstitute germ-free recipients – Zachary L McAdams – Gut Microbes Reports

Bacterial microbiome diversity along poultry slaughtering lines: insights from chicken carcasses and environmental sources – Arife Ezgi Telli – Journal of Veterinary Research

The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus – Gregorio Fernandez de Landa – Microbial Ecology

Gill-associated ammonia oxidizers are widespread in teleost fish – Wouter Mes – Microbiology Spectrum

Microbiome Analysis: Methods, Tools and Resources

Automated annotation of scientific texts for ML-based keyphrase extraction and validation – Oluwamayowa O Amusat – Database

SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota – Johanna B Holm – BMC Bioinformatics

Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction – Veronika Andriienko – PeerJ

A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples – Krystal Thomas-White – Diagnostics

Microbe-drug association prediction model based on graph convolution and attention networks – Bo Wang – Scientific Reports

September 26, 2024

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General microbiome

[RESOURCE/COLLECTION]Microbial Primers

Phages reconstitute NAD+ to counter bacterial immunity – Osterman et al. – Nature

The direct inhibitory effects of Lactobacillus acidophilus, a commensal urinary bacterium, on calcium oxalate stone development – Noonin et al. – Microbiome

Pregnancy and early life

Neonatal gut microbiota profile and the association with retinopathy of prematurity in preterm infants – Chang et al. – Clinical & Experimental Ophthalmology

Human skin microbiome

The wound microbiota: microbial mechanisms of impaired wound healing and infection – Uberoi, McCready-Vangi, Grice – Nature Reviews Microbiology

Human oral microbiome

[PREPRINT]Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition – Zelasko et al. – bioRxiv

Human gut microbiome

Emergence of community behaviors in the gut microbiota upon drug treatment – Garcia-Santamarina et al. – Cell

Microbial transformation of dietary xenobiotics shapes gut microbiome composition – Culp et al. – Cell

[REVIEW]Microglia and Gut Microbiota: A Double-Edged Sword in Alzheimer’s Disease – Bano et al. – Ageing Research Reviews

[REVIEW]What defines a healthy gut microbiome? – van Hul et al. – Gut

[OUTLOOK]The gut microbiome and chronic pain – Watson – Nature

Acarbose enhances the efficacy of immunotherapy against solid tumours by modulating the gut microbiota – Zhang et al. – Nature Metabolism

Animal microbiome (for animals in the wild)

Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores – Li et al. – Microbiome

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

Microbial community storm dynamics signal sources of “old” stream water – URycki et al. – PLOS One

Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments – Lezcano et al. – Microbiome

Food microbiology

Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history – Liu et al. – Cell

Bioinformatics

A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies – Wirbel et al. – Genome Biology

[PREPRINT]Quantifying Data Distortion in Bar Graphs in Biological Research – Lin & Landry – bioRxiv

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 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 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

June 2, 2024

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Human Microbiome

Commensal bacterial outer membrane protein A induces interleukin-22 production – Yanling Wang – Cell Reports

Mucus production, host-microbiome interactions, hormone sensitivity, and innate immune responses modeled in human cervix chips – Zohreh Izadifar – Nature Communications

Gut microbiome and symptoms in females with irritable bowel syndrome: a cross-sectional analysis – K J Kamp – Beneficial Microbes

Gut microbiome in the Graves’ disease: Comparison before and after anti-thyroid drug treatment – Chaiho Jeong – PloS ONE

Guild-level signature of gut microbiome for diabetic kidney disease – Shasha Tang – mBio

Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study – JooHee Choi – EClinicalMedicine

Gut microbiota-derived butyrate induces epigenetic and metabolic reprogramming in myeloid-derived suppressor cells to alleviate primary biliary cholangitis – Rui Wang – Gastroenterology

Review: Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes – Yuhao Fu – mLife

Review: Exploring the Impact of Airway Microbiome on Asthma Morbidity: A Focus on the Constructing a ‘Eubiosis Reinstatement Therapy’ for Asthma-CURE Project – Paraskevi Xepapadaki – Pulmonary Therapy

Beneficial Microbes and Compounds

A Gram-negative-selective antibiotic that spares the gut microbiome – Kristen A Muñoz – Nature

Bifidobacterium adolescentis-derived hypaphorine alleviates acetaminophen hepatotoxicity by promoting hepatic Cry1 expression – Ping Qin – Journal of Translational Medicine

Chrysanthemum morifolium attenuates metabolic and alcohol-associated liver disease via gut microbiota and PPARα/γ activation – Dan Liu – Phytomedicine

Animal Model Microbiome

Transgenerational effects of early life stress on the fecal microbiota in mice – Nize Otaru – Communications Biology

Metagenomics and metaproteomics alterations are associated with kidney disease in opisthorchiasis hamsters fed a high-fat and high-fructose diet – Keerapach Tunbenjasiri – PloS ONE

Animal Microbiome

Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats – Qingyong Hu – Applied Microbiology and Biotechnology

Interaction between methanotrophy and gastrointestinal nematodes infection on the rumen microbiome of lambs – Patricia Spoto Corrêa – FEMS Microbiology Ecology

Antibiotic-altered gut microbiota explain host memory plasticity and disrupt pace-of-life covariation for an aquatic snail – Gabrielle L Davidson – The ISME Journal

Food Microbiome

Metagenome-assembled genomes from microbiomes fermenting dairy coproducts – Kevin A Walters – Microbiology Resource Announcements

Environmental Microbiome

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

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling – Zhepu Ruan – Nature Communications

Interpretable machine learning decodes soil microbiome’s response to drought stress – Michelle Hagen – Environmental Microbiome

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

Microbiome Analysis

Combining compositional data sets introduces error in covariance network reconstruction – James D Brunner – ISME Communications

How to Obtain and Compare Metagenome-Assembled Genomes – Fabio Beltrame Sanchez – Methods in Molecular Biology

A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros – Fentaw Abegaz – Scientific Reports

Review: A review of machine learning methods for cancer characterization from microbiome data – Marco Teixeira – NPJ Precision Oncology

May 15, 2024

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Human gut microbiome

A shared group of bacterial taxa in the duodenal microbiota of undernourished Pakistani children with environmental enteric dysfunction – Najeeha T Iqbal – mSphere

Gut microbiota, blood metabolites, and left ventricular diastolic dysfunction in US Hispanics/Latinos – Kai Luo – BMC Microbiome

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Xuanji Li – BMC Microbiome

Impact of the gut microbiome composition on social decision-making – Marie Falkenstein – PNAS Nexus

Veillonella and Bacteroides are associated with gestational diabetes mellitus exposure and gut microbiota immaturity – Fernanda Valdez-Palomares – PLOS One

[REVIEW] The neonatal gut microbiome and global health – Pinaki Panigrahi – Gut Microbes

Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation – Shusan Sargisan – BMC Microbiome

Vaginal microbiome

16S rRNA female reproductive microbiome investigation reveals Dalfopristin, Clorgyline, and Hydrazine as potential therapeutics for the treatment of bacterial vaginosis – Sudeepti Kulshrestha – Diagnostic Microbiology and Infectious Disease

Fecal transplant from vaginally seeded infants decreases intraabdominal adiposity in mice – Sivaranjani Namasivayam – Gut Microbes

Animal microbiome

Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits – Ming Yan & Zhongtang Yu – BMC Microbiome

Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA) – David B. Carlini – Nature Scientific Reports

How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast – Ryoko Oono – Environmental Microbiology

Beneficial microbes & compounds

The gut lactic acid bacteria metabolite, 10-oxo- cis-6, trans-11-octadecadienoic acid, suppresses inflammatory bowel disease in mice by modulating the NRF2 pathway and GPCR-signaling – Miki Ando – Frotiers in Immunology

Effect of weight loss program using prebiotics and probiotics on body composition, physique, and metabolic products: longitudinal intervention study – Nayera E Hassan – Nature Scientific Reports

Origin of the neonatal gut microbiota and probiotic intervention: a randomized controlled trial – Zhe Li – Frontiers in Nutrition

Effectiveness of probiotic- and fish oil-loaded water-in-oil-in-water (W1/O/W2) emulsions at alleviating ulcerative colitis – Qingzhao Gu – Food & Function

Plant, root, and soil microbiome

Competition mode and soil nutrient status shape the role of soil microbes in the diversity–invasibility relationship – Haokun Li – Ecology and Evolution

Dynamics and drivers of fungal communities in a multipartite ant-plant association – Veronica Barrajon-Santos – BMC Biology

Quorum sensing related activities of beneficial and pathogenic bacteria have important implications for plant and human health – Anton Hartmann – FEMS Microbiology Ecology

Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems – Geoffrey S. Siemering – Water Environment Research

Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly – Caroline Sayuri Nishisaka – BMC Environmental Microbiome

The predominant lactic acid bacteria and yeasts involved in the spontaneous fermentation of millet during the production of the traditional porridge Hausa koko in Ghana – Amy Atter – BMC Microbiology

Bioinformatics & Tools

Multi-class boosting for the analysis of multiple incomplete views on microbiome data – Andrea Simeon – BMC Bioinformatics

PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome – Lara Vázquez-González – BMC Bioinformatics

Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches – Ryan Kuster – BMC Bioinformatics