Category Archives: Human gut

August 18, 2024

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Human and General Microbiome

Maternal antibiotic prophylaxis during cesarean section has a limited impact on the infant gut microbiome – Trishla Sinha – Cell Host & Microbe

Microbial assimilatory sulfate reduction-mediated H(2)S: an overlooked role in Crohn’s disease development – Wanrong Luo – Microbiome (BMC)

Characterization of the vaginal microbiota in Italian women with endometriosis: preliminary study – Rosa Sessa – Archives of Gynecology and Obstetrics

Profiles and interactions of gut microbiome and intestinal microRNAs in pediatric Crohn’s disease – Yao Lv – mSystems

Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut – Qiong Wu – Food Research International

Review: Effects of physical exercise on Akkermansia muciniphila: a systematic review of human and animal studies – S S Aguiar – Beneficial Microbes

Beneficial Microbes and Compounds

Commentary: Microbiome modification for personalized treatment of dysbiotic diseases – R Balfour Sartor – Cell Host & Microbe

Combining Gut Microbiota Modulation and Enzymatic-Triggered Colonic Delivery by Prebiotic Nanoparticles Improves Mouse Colitis Therapy – Hui Li – Biomaterials Research

Animal Microbiome

Effect of chronic alcohol consumption on oral microbiota in rats with periodontitis – Zirui Zhao – PeerJ

Fecal microbiota transplantation accelerates restoration of florfenicol-disturbed intestinal microbiota in a fish model – Zhuoran Han – Communications Biology

Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen – Robert J Gruninger – The Protein Journal

Plant Microbiome

Review: Harnessing the plant microbiome for sustainable crop production – Stéphane Compant – Nature Reviews Microbiology

Review: The impact of filamentous plant pathogens on the host microbiota – Victor M Flores-Nunez – BMC Biology

Environmental Microbiome

Metagenomic insights into the prokaryotic communities of heavy metal-contaminated hypersaline soils – Cristina Galisteo – The Science of the Total Environment

Ecological phage therapy: Can bacteriophages help rapidly restore the soil microbiome? – Tarryn Davies – Ecology and Evolution

Do restoration strategies in mangroves recover microbial diversity? A case study in the Yucatan peninsula – Daniel Esguerra-Rodríguez – PloS One

Metagenome sequencing and 107 microbial genomes from seamount sediments along the Yap and Mariana trenches – Yue Zhang – Scientific Data

Microbiome Analysis: Tools, Techniques and Resources

Metrological evaluation of DNA extraction method effects on the bacterial microbiome and resistome in sputum – Aleksander Benčič – mSystems

Commentary: AI in microbiome research: Where have we been, where are we going? – Georg K Gerber – Cell Host & Microbe

Review: Modeling Microbial Communities: Perspective and Challenges – Lavanya Raajaraam – ACS Synthetic Biology

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 6, 2024

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Human Gut Microbiota

Review – The role of the gut microbiota in regulating responses to vaccination: current knowledge and future directions – Rossouw et al. FEBS

Systemic antibody responses against gut microbiota flagellins implicate shared and divergent immune reactivity in Crohn’s disease and chronic fatigue syndrome – Bourgonje et al. – Microbiome

Pregnancy and early life

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

Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics – Leech et al. Microbial Genomics.

Association of breast milk-derived arachidonic acid-induced infant gut dysbiosis with the onset of atopic dermatitis – Jiang et al. – Gut

General Human Microbiota

The potential role of lung microbiota and lauroylcarnitine in T-cell activation associated with checkpoint inhibitor pneumonitis – Yu et al. eBioMedicine

Evidence of Lactobacillus strains shared between the female urinary and vaginal microbiota – Atkins et al. – Microbial Genomics

A human commensal-pathogenic fungus suppresses host immunity via targeting TBK1 – Lou et al. Cell Host & Microbe

Bacteriophage

Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses – Van den Berg et al. – Cell Host & Microbe

Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses – Stiffler et al. – Microbiome

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

August 01, 2024

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Pregnancy and early life

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

Built environment (subways, indoor surfaces)

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

Bioinformatics

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

July 31, 2024

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Human gut microbiome

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

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

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

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

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

Animal experiments

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

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

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

Animal microbiome

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

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

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

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

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

Beneficial microbes and compounds

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

Plant, root, and soil microbiome

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

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

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

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

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 25, 2024

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Pregnancy and early life

Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth – Johnson et al. – Nature Communications

[PREPRINT]First-Year Dynamics of the Anaerobic Microbiome and Archaeome in Infants Oral and Gastrointestinal Systems – Neumann et al. – bioRxiv

Human skin microbiome

A Mendelian randomization analysis reveals the multifaceted role of the skin microbiota in liver cancer – Wang & Zhu – Frontiers in Microbiology

Metagenomic sequencing of the skin microbiota of the scalp predicting the risk of surgical site infections following surgery of traumatic brain injury in sub-Saharan Africa – Lekuya et al. – PLOS One

Human gut microbiome

[REVIEW]The interplay between diet and the gut microbiome: implications for health and disease – Ross et al. – Nature Reviews Microbiology

Microbiota composition effect on immunotherapy outcomes in colorectal cancer patients: A systematic review – Ajab et al. – PLOS One

Animal microbiome

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

Effect of soybean and seaweed-based diets on growth performance, feed utilization, and gut microbiota of tilapia: A systematic review and meta-analysis – Viagem et al. – PLOS One

Plant, root, and soil microbiome

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

Phages and viruses

Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer – Ivancevic et al. – Science Advances

The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort – Ma et al. – Microbiome

Viruses of free-roaming and hunting dogs in Uganda show elevated prevalence, richness and abundance across a gradient of contact with wildlife – Tayebwa et al. – Journal of General Virology