Tag Archives: Animal 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 11, 2024

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Human and General Microbiome

B cell senescence promotes age-related changes in oral microbiota – Hiroya Mizuno – Aging Cell

Exploring the relationship between gut microbiota and breast cancer risk in European and East Asian populations using Mendelian randomization – Wei Lin – BMC Cancer

Intratumoral microbiome promotes liver metastasis and dampens adjuvant imatinib treatment in gastrointestinal stromal tumor – Yanze Li – Cancer Letters

Comparison of Vaginal microbiota in HPV-negative and HPV-positive pregnant women using a culture-based approach – Podoprigora Irina – Diagnostic Microbiology and Infectious Disease

The gut-microbiome in adult Attention-deficit/hyperactivity disorder – A Meta-analysis – Babette Jakobi – European Neuropsychopharmacology

An Empirical Dietary Pattern Associated with the Gut Microbial Features in Relation to Colorectal Cancer Risk – Kai Wang – Gastroenterology

Species-level characterization of gut microbiota and their metabolic role in kidney stone formation using full-length 16S rRNA sequencing – Bashir Hussain – Urolithiasis

Review: Game of microbes: the battle within – gut microbiota and multiple sclerosis – Ti-Ara Turner – Gut Microbes

Review: The early life exposome and autism risk: a role for the maternal microbiome? – Claudia M Di Gesù – Gut Microbes

Review: Gut mycobiome alterations and implications for liver diseases – Suling Zeng – PLoS Pathogens

Beneficial Microbes and Compounds

A novel intervention of molecular hydrogen on the unbalance of the gut microbiome in opioid addiction: Experimental and human studies – Bing Xie – Biomedicine & Pharmacotherapy

Lower fecal microbiota transplantation ameliorates ulcerative colitis by eliminating oral-derived Fusobacterium nucleatum and virulence factor – Dong-Hao Li – Gut Pathogens

Induction of Cell Death by Bifidobacterium infantis DS1685 in Colorectal and Breast Cancers via SMAD4/TGF-Beta Activation – In Hwan Tae – Journal of Microbiology and Biotechnology

Review: Peptide GLP-1 receptor agonists: From injection to oral delivery strategies – Zhiqiang Ke – Biochemical Pharmacology

Animal Microbiome (including model experiments)

Stress-sensitive neural circuits change the gut microbiome via duodenal glands – Hao Chang – Cell

Effect of Hafnia alvei on Morphophysiologic Parameters and Gut Microbiota of Mice with Inherited Type 2 Diabetes Mellitus – V A Zolotarev – Bulletin of Experimental Biology and Medicine

Spatial analysis of murine microbiota and bile acid metabolism during amoxicillin treatment – Chapman N Beekman – Cell Reports

Evaluating impacts of radiation-induced sterilization on the performance and gut microbiome of mass-reared Mediterranean fruit fly (Ceratitis capitata) in Hawai’i – Charles J Mason – Journal of Economic Entomology

Plant Microbiome

Disease Resistance Correlates with Core Microbiome Diversity in Cotton – Rhea Aqueel – Current Microbiology

Environmental Microbiome

The symbiotic alga Trebouxia fuels a coherent soil ecosystem on the landscape scale in the Atacama Desert – Patrick Jung – Environmental Microbiome

Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone – Alexandre Barretto de Menezes – The Science of the Total Environment

The first large scale rDNA amplicon database of soil microbiomes from Pamir Plateau, China – Jing Zhu – Scientific Data

Food and Beverage Microbiome

Changes in the solid-associated bacterial and fungal communities following ruminal in vitro fermentation of winery by-products: aspects of the bioactive compounds and feed safety – Ratchaneewan Khiaosa-Ard – Anaerobe

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

Analyzing the gut microbiota and microbial-associated metabolites of tomato-based sauces – Alicia Paulina Cárdenas-Castro – Food Chemistry

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 4, 2024

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Human Gut Microbiome

Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV – Aswathy Narayanan – Scientific Reports

Human Gut Microbiota Composition Associated with International Travels – D Henares – Travel Medicine and Infectious Disease

Respiratory microbiome and clinical course of carbapenem-resistant Acinetobacter baumannii pneumonia in critically Ill patients – Jin Gu Yoon – Medicine

Review: Gut Microbiota and Autism Spectrum Disorder: A Neuroinflammatory Mediated Mechanism of Pathogenesis? – Fatemeh Zarimeidani – Inflammation

Review: Gut microbiota and eating behaviour in circadian syndrome – Jorge R Soliz-Rueda – Trends in Endocrinology and Metabolism

Beneficial Microbes and Compounds

Staphylococcus aureus/Staphylococcus epidermidis from skin microbiota are balanced by Pomegranate peel extract: An eco-sustainable approach – Sara D’Arcangelo – PloS One

Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities – Francesca De Filippis – NPJ Biofilms and Microbiomes

Bugs as drugs: Extended clinical applications and potential translational trends of Akkermansia muciniphila in oncology and comprehensive clinical investigation panorama of therapeutic microbiome modulators in gastric cancer treatment – Yuning Wang – Pharmacological Research

Polyphenols: potent protectors against chronic diseases – Geetha Shanmugam – Natural Product Research

Animal Microbiome

Effects of berberine hydrochloride on antioxidant response and gut microflora in the Charybdis japonica infected with Aeromonas hydrophila – Mingming Han – BMC Microbiology

Design of an agro-industrial by-products-based media for the production of probiotic bacteria for fish nutrition – Marcelo Fernando Valle Vargas – Scientific Reports

Association of microbial community structure with gill disease in marine-stage farmed Atlantic salmon (Salmo salar); a yearlong study – Morag Clinton – BMC Veterinary Research

Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles – Torsten Nygaard Kristensen – Scientific Reports

Novel insights on microbiome dynamics during a gill disease outbreak in farmed rainbow trout (Oncorhynchus mykiss) – Samuele Zamparo – Scientific Reports

Gut Microbiome-Driven metabolites influence skin pigmentation in TYRP1 mutant Oujiang color common carp – Roland Nathan Mandal – Gene

Plant and Soil Microbiome

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology – Winston E Anthony – Environmental Microbiome

An acidophilic fungus promotes prey digestion in a carnivorous plant – Pei-Feng Sun – Nature Microbiology

A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress – Jianfeng Zhang – The Science of the Total Environment

A bud’s life: Metabarcoding analysis to characterise hazelnut big buds microbiome biodiversity – Silvia Turco – Microbiological Research

Perspective: Integrating viruses into soil food web biogeochemistry – Cátia Carreira – Nature Microbiology

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

Environmental Microbiome

Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses – Alexandra K Stiffler – Microbiome

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

July 28, 2024

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Human and General Microbiome

Shaping Microbiota During the First 1000 Days of Life – Anna Samarra – Advances in Experimental Medicine and Biology

Role of sulfidogenic members of the gut microbiota in human disease – Andreia I Pimenta – Advances in Microbial Physiology

Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor – Yunjae Kim – Cell Host & Microbe

Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort – Taona Emmah Mudhluli – BMC Genomics

Gut microbial features and circulating metabolomic signatures of frailty in older adults – Yanni Pu – Nature Aging

Gut microbiome and metabolome signatures in liver cirrhosis-related complications – Satya Priya Sharma – Clinical and Molecular Hepatology

Detection of Microplastics in Human Breast Milk and Its Association with Changes in Human Milk Bacterial Microbiota – Apisith Saraluck – Journal of Clinical Medicine

Regional Differences in Microbial Infiltration of Brain Tissue from Alzheimer’s Disease Patients and Control Individuals – T Bucky Jones – Brain Sciences

Review: Aggregatibacter actinomycetemcomitans: From the Oral Cavity to the Heart Valves – Jasminka Talapko – Microorganisms

Beneficial Microbes and Compounds

Review: Digesting the complex metabolic effects of diet on the host and microbiome – Rachel N Carmody – Cell

Review: A comprehensive review of synbiotics: an emerging paradigm in health promotion and disease management – Sulhee Lee – World Journal of Microbiology & Biotechnology

Animal Model Microbiome

Desulfovibrio vulgaris caused gut inflammation and aggravated DSS-induced colitis in C57BL/6 mice model – Guoxin Huang – Gut Pathogens

LCN2 regulates the gut microbiota and metabolic profile in mice infected with Mycobacterium bovis – Quntao Huang – mSystems

Non-Model Animal Microbiome

Multiomics of parkinsonism cynomolgus monkeys highlights significance of metabolites in interaction between host and microbiota – Jiang-Mei Gao – NPJ Biofilms and Microbiomes

Vaginal and Uterine Microbiota of Healthy Maiden Mares during Estrus – Ana Gil-Miranda – Veterinary Sciences

Review: Reproductive Tract Microbiota of Mares – Ana Gil-Miranda – Veterinary Sciences

Environmental Microbiology

Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances – Mafalda S Baptista – Environmental Microbiome

Plant Microbiome

Thermal sensitivity of soil microbial carbon use efficiency across forest biomes – Chengjie Ren – Nature Communications

Miscanthus sp. root exudate alters rhizosphere microbial community to drive soil aggregation for heavy metal immobilization – Bohan Wu – The Science of the Total Environment

Soil conditions modify species diversity effects on tree functional trait expression – Andréa Davrinche – Scientific Reports

Microbiome Analysis

A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction – Tatiana Y Fofanova – PloS ONE

Compositional Data and Microbiota Analysis: Imagination and Reality – Tatsuki Itagaki – Microorganisms

Thanos: An R Package for the Gene-Centric Analysis of Functional Potential in Metagenomic Samples – Zhe Zhao – Microorganisms

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

July 21, 2024

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Human and General Microbiome

Akkermansia muciniphila and Parabacteroides distasonis as prognostic markers for relapse in ulcerative colitis patients – Ana Mendes-Frias – Frontiers in Cellular and Infection Microbiology

Obesity-enriched gut microbe degrades myo-inositol and promotes lipid absorption – Chao Wu – Cell Host & Microbe

Gut microbiome in endometriosis: a cohort study on 1000 individuals – Inmaculada Pérez-Prieto – BMC Medicine

Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer – Pan Zhang – Journal of Medical Virology

The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors – Caroline E Dravillas – Cancer Research Communications

Gut microbiome diversity within Clostridia is negatively associated with human obesity – Laura Salazar-Jaramillo – mSystems

Early depletion of gut microbiota shape oligodendrocyte response after traumatic brain injury – Kirill Shumilov – Journal of Neuroinflammation

Effect of progestin-based contraceptives on HIV-associated vaginal immune biomarkers and microbiome in adolescent girls – Mélodie A Nasr – PloS One

Review: Microbiome and pancreatic cancer: time to think about chemotherapy – Juliana de Castilhos – Gut Microbes

Review: Host control of the microbiome: Mechanisms, evolution, and disease – Jacob Wilde – Science

Review: Connecting microbial community assembly and function – Leonora S Bittleston – Current Opinion in Microbiology

Review: Microbiota of Saliva: A Non-invasive Diagnostic Tool – Dasharath B Shinde – Indian Journal of Microbiology

Beneficial Microbes, Compounds and Interventions

Topical prebiotic nitrate: optimizing the ‘hang-time’, source and dose for specific oral or systemic effects – Bob T Rosier – NPJ Biofilms and Microbiomes

An improved diet-based nutritional interventions can improve childhood obesity with the synergistic regulation of gut microbiota – M Zhou – Beneficial Microbes

Intermittent fasting, calorie restriction, and a ketogenic diet improve mitochondrial function by reducing lipopolysaccharide signaling in monocytes during obesity: A randomized clinical trial – Martha Guevara-Cruz – Clinical Nutrition 

Food Microbiome

Influence of the initial microbiota on eggplant shibazuke pickle and eggplant juice fermentation – Kazunori Sawada – Microbiology Spectrum

Metatranscriptomics reveals microbial community function succession and characteristic flavor formation mechanisms during black rice wine fermentation – Aoxing Tang – Food Chemistry

Animal Model Microbiome

Gα13 restricts nutrient driven proliferation in mucosal germinal centers – Hang T Nguyen – Nature Immunology

Gut microbiota mediates ambient PM(2.5) exposure-induced abnormal glucose metabolism via short-chain fatty acids – Wenpu Shao – Journal of Hazardous Materials

Non-Model Animal Microbiome

Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants – Christian Cabuslay – Molecular Ecology

Review: The interplay between gut symbionts and behavioral variation in social insects – Joanito Liberti – Current Opinion in Insect Science

Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease – Wei-Chen Wu – mSphere

Alcohol consumption during pregnancy differentially affects the fecal microbiota of dams and offspring – Tamara S Bodnar – Scientific Reports

Environmental Microbiome

Meta-omics analysis reveals the marine arsenic cycle driven by bacteria – Zhao-Jie Teng – Journal of Hazardous Materials

Using Machine Learning to Identify Environmental Factors that Collectively Determine Microbial Community Structure of Activated Sludge – Lu Wang – Environmental Research

Microplastic pollution promotes soil respiration: A global-scale meta-analysis – Shuling Zhao – Global Change Biology

SMMP: A Deep-Coverage Marine Metaproteome Method for Microbial Community Analysis throughout the Water Column Using 1 L of Seawater – Songduo Wang – Analytical Chemistry

Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau – Luyao Kang – Nature Communications

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass – Xuejiao Lyu – Journal of Industrial Microbiology & Biotechnology

Microbiome Analysis

GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs – Jianshu Zhao – Nucleic Acids Research

Multi-omics machine learning to study host-microbiome interactions in early-onset colorectal cancer – Thejus T Jayakrishnan – NPJ Precision Oncology

3D printed rectal swabs for assessing the gut microbiome, metabolome and inflammation – Robert W Perry – Scientific Reports

AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides – Amin Darabi – BMC Bioinformatics

JASPER: Fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression – Joelle Mbatchou – American Journal of Human Genetics

Microbial Evolution

The nature of the last universal common ancestor and its impact on the early Earth system – Edmund R R Moody – Nature Ecology & Evolution

June 30, 2024

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Human and General Microbiome

Gut

Metaproteomic portrait of the healthy human gut microbiota – Alessandro Tanca – NPJ Biofilms and Microbiomes

Microbiome and Growth in Infants with Congenital Heart Disease – Michael P Fundora – The Journal of Pediatrics

Driving gut microbiota enterotypes through host genetics – Catherine Larzul – Microbiome

Obesity-associated microbiomes instigate visceral adipose tissue inflammation by recruitment of distinct neutrophils – Dharti Shantaram – Nature Communications

Fecal, Duodenal and Tumor Microbiota Composition of Esophageal Carcinoma Patients, a Longitudinal Prospective Cohort – Tom van den Ende – Journal of the National Cancer Institute

Review: Role of the intestinal microbiota in contributing to weight disorders and associated comorbidities – Matthias Van Hul – Clinical Microbiology Reviews

Review: The role of the gut microbiome in disorders of gut-brain interaction – Brent J Gawey – The FEBS Journal

Skin

Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin – Tianze Yu – Cell Host & Microbe

Genitourinary Tract

Vaginal anaerobes are associated with cervicitis: a case-control study – Erica L Plummer – The Journal of Infection

Oral and Respiratory Tract

Review: The Impact of Oral Diseases on Respiratory Health and the Influence of Respiratory Infections on the Oral Microbiome – Annapurna Gupta – Journal of Dentistry

Beneficial Microbes and Compounds

Lactobacillus acidophilus protects against Corynebacterium pseudotuberculosis infection by regulating the autophagy of macrophages and maintaining gut microbiota homeostasis in C57BL/6 mice – Dengliang Li – mSystems

Exploring novel microbial metabolites and drugs for inhibiting Clostridioides difficile – Ahmed A Abouelkhair – mSphere

Ketogenic diet-induced bile acids protect against obesity through reduced calorie absorption – Xiao Li – Nature Metabolism

Review: How Diet and Lifestyle Can Fine-Tune Gut Microbiomes for Healthy Aging – M Tamayo – Annual Review of Food Science and Technology

Animal Microbiome

Gut microbiota signatures of vulnerability to food addiction in mice and humans – Solveiga Samulėnaitė – Gut

Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate – Peter M Finnegan – mSphere

Maternal transmission as a microbial symbiont sieve, and the absence of lactation in male mammals – Brennen T Fagan – Nature Communications

Built Environment Microbiome

A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal – Sarbanding Sané – Scientific Reports

Microbiome Analysis: Tools, Techniques and Resources

Compositionally aware estimation of cross-correlations for microbiome data – Ib Thorsgaard Jensen – PloS ONE

Bioinformatic Workflows for Metaproteomics – Tanja Holstein – Methods in Molecular Biology 

Floria: fast and accurate strain haplotyping in metagenomes – Jim Shaw – Bioinformatics 

Enhancing antimicrobial resistance detection with MetaGeneMiner: Targeted gene extraction from metagenomes – Chang Liu – Chinese Medical Journal

Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics – Alessandro Tanca – mSystems

Genome Watch: Bacterial barcoding facilitates plant microbiome studies – Hualan Liu – Nature Reviews Microbiology

Other

Retraction Note: Microbiome analyses of blood and tissues suggest cancer diagnostic approach – Gregory D Poore – Nature

June 23, 2024

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Human and General Microbiome

Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome – Lisa Derosa – Cell

News: Gut microbiome discovery provides roadmap for life-saving cancer therapies – Giorgia Guglielmi – Nature

Faecal microbiota transplantation for sleep disturbance in post-acute COVID-19 syndrome – Raphaela I Lau – Clinical Gastroenterology and Hepatology

Pan-cancer atlas of tumor-resident microbiome, immunity and prognosis – Dashuang Sheng – Cancer Letters

Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers – Anju R Nath – Genomics & Informatics

A Bioinformatic Analysis of Gut Microbiota Related with Immune Cell Infiltration in Colorectal Cancer – Dan Liu – Cancer Investigation

An alternative broad-specificity pathway for glycan breakdown in bacteria – Seyed Amirhossein Nasseri – Nature

The association of maternal factors with the neonatal microbiota and health – Bin Zhu – Nature Communications

Revealing the gut microbiome mystery: A meta-analysis revealing differences between individuals with autism spectrum disorder and neurotypical children – Changjiang Yang – Bioscience Trends

Propionic acid promotes neurite recovery in damaged multiple sclerosis neurons – Barbara Gisevius – Brain Communications

Review: What is the impact of microbiota on dry eye: a literature review of the gut-eye axis – Jiaping Song – BMC Ophthalmology

Review: Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health – Meifang Xiao – NPJ Biofilms and Microbiomes

Review: Peyer’s Patch: Possible target for modulating the Gut-Brain-Axis through microbiota – Reza Asgari – Cellular Immunology

Animal Model Microbiome

Alterations in gut microbiota and inflammatory cytokines after administration of antibiotics in mice – Wang Gao – Microbiology Spectrum

Environmental Microbiome

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts – Emily B Graham – Nature Microbiology

Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome – Emanuela Buschi – Science Advances

Microbial co-occurrence network demonstrates spatial and climatic trends for global soil diversity – Nikos Pechlivanis – Scientific Data

Other Microbes

Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries – Felipe Senne de Oliveira Lino – Nature Communications

Microbiome Analysis: tools, techniques and resources

A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome – Liansha Huang – Nature Microbiology

Deep learning for predicting 16S rRNA gene copy number – Jiazheng Miao – Scientific Reports

GEM-based computational modeling for exploring metabolic interactions in a microbial community – Soraya Mirzaei – PLoS Computational Biology

Review: Techniques, procedures, and applications in microbiome analysis – Adriana González – Advances in Genetics