May 29, 2024

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Human microbiomes

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

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

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

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

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

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

Animal microbiome

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

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

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

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

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

Food microbiome

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

Plant, soil, and root microbiome

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

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

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

Water & extremophile microbiome

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

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

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

May 26, 2024

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Human Microbiome in General

Microbiome research in Africa must be based on equitable partnerships – Ovokeraye H Oduaran – Nature Medicine

Human Gut Microbiome

IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota – Ivo Röwekamp – PNAS

Meta-analysis of shotgun sequencing of gut microbiota in Parkinson’s disease – Hiroshi Nishiwaki – NPJ Parkinson’s Disease

Systematic review of associations between gut microbiome composition and stunting in under-five children – Mwelwa Chibuye – NPJ Biofilms and Microbiomes

Production of deoxycholic acid by low-abundant microbial species is associated with impaired glucose metabolism – Annika Wahlström – Nature Communications

Altered gut microbiota is associated with the formation of occult hepatitis B virus infection – Bochao Liu – Microbiology Spectrum

Metagenome-assembled genomes (MAGs) suggest an acetate-driven protective role in gut microbiota disrupted by Clostridioides difficile – Giovanny Herrera – Microbiological Research

Review: From gut microbiota to brain: implications on binge eating disorders – Weiwei Guo – Gut Microbes

Review: Pathogenesis and therapeutic opportunities of gut microbiome dysbiosis in critical illness – Nicole A Cho – Gut Microbes

Human Respiratory Tract Microbiome

Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation – Matt S Zinter – Nature Medicine

Human Genitourinary Tract Microbiome

Leveraging existing 16S rRNA gene surveys to decipher microbial signatures and dysbiosis in cervical carcinogenesis – Xiaoxiao Li – Scientific Reports

Targeting Megasphaera species to promote cervicovaginal health – Mariano A Molina – Trends in Microbiology

Beneficial Microbes and Compounds

Prodrug-conjugated tumor-seeking commensals for targeted cancer therapy – Haosheng Shen – Nature Communications

Fecal microbiota transplantation significantly improved respiratory failure of amyotrophic lateral sclerosis – Jingshuang Yan – Gut Microbes

The use of probiotics and prebiotics in decolonizing pathogenic bacteria from the gut; a systematic review and meta-analysis of clinical outcomes – Md Nannur Rahman – Gut Microbes

Review: Advanced microbiome therapeutics as a novel modality for oral delivery of peptides to manage metabolic diseases – Ruben Vazquez-Uribe – Trends in Endocrinology and Metabolism

Animal Microbiome

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

Symbiotic bacteria and fungi proliferate in diapause and may enhance overwintering survival in a solitary bee – Shawn M Christensen – The ISME Journal

Plant Microbiome

Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness – Xiaofang Wang – mBio

Environmental Microbiome

Global epistasis and the emergence of function in microbial consortia – Juan Diaz-Colunga – Cell

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution – Brune Joannard – Microbiome

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

A global initiative for ecological and evolutionary hologenomics – Aoife Leonard – Trends in Ecology & Evolution

Built Environment Microbiome

Fungal diversity differences in the indoor dust microbiome from built environments on earth and in space – Nicholas Nastasi – Scientific Reports

Microbiome Analysis: Tools, Techniques and Resources

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease – Katherine Do – mSphere

A comparative study of supervised and unsupervised machine learning algorithms applied to human microbiome – E Kalluçi – La Clinica Terapeutica

May 19, 2024

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Human Gut Microbiome

Genetic association between gut microbiome and blood pressure and blood cell count as mediator: A two-step Mendelian randomization analysis – Jiyu Zhang – Gene

Characterization of the gut microbiota in polycystic ovary syndrome with dyslipidemia – Tianjin Yang – BMC Microbiology

Environmental Factors Associated with Risk of Crohn’s Disease Development in the CCC-GEM Project – Mingyue Xue – Clinical Gastroenterology and Hepatology

Cohort profile of an early life observational cohort in China: Bone and MicroBiOme onset (BAMBOO) study – Jing Wang – BMJ Open

Framework for exploring the sensory repertoire of the human gut microbiota – Patricia A Ross – mBio

Metformin-induced changes of the gut microbiota in patients with type 2 diabetes mellitus: results from a prospective cohort study – Yuting Gao – Endocrine

Review: Host-microbiota interaction in intestinal stem cell homeostasis – Haiqin Wu – Gut Microbes

Review: Gut dysbiosis and neurological modalities: An engineering approach via proteomic analysis of gut-brain axis – Meenakshi Kandpal – Advances in Protein Chemistry and Structural Biology

Human Respiratory Tract Microbiome

Comparative microbiome analysis in cystic fibrosis and non-cystic fibrosis bronchiectasis – Heryk Motta – Respiratory Research

Indole-3-Acetic Acid Protects Against Lipopolysaccharide-induced Endothelial Cell Dysfunction and Lung Injury through the Activation of USP40 – Nargis Shaheen – American Journal of Respiratory cell and Molecular Biology

Human Oral Microbiome

Quantitative analysis of the effects of brushing, flossing, and mouthrinsing on supragingival and subgingival plaque microbiota: 12-week clinical trial – Kyungrok Min – BMC Oral Health

Human Skin Microbiome

Review: Exploring the skin microbiome in atopic dermatitis pathogenesis and disease modification – Claudia Hülpüsch – The Journal of Allergy and Clinical Immunology

Beneficial Microbes and Compounds

Isobutyric acid enhances the anti-tumour effect of anti-PD-1 antibody – Masakazu Murayama – Scientific Reports

Effects of fructooligosaccharides and Saccharomyces boulardii on the compositional structure and metabolism of gut microbiota in students – Hao Fu – Microbiological Research

Urolithin A’s Role in Alleviating Severe Acute Pancreatitis via Endoplasmic Reticulum-Mitochondrial Calcium Channel Modulation – Hongxin Kang – ACS Nano

Animal Model Microbiome

Oral microbiota transplantation for intra-oral halitosis: a feasibility analysis based on an oral microbiota colonization trial in Wistar rats – Zhiqiang Huang – BMC Microbiology

NOD2 contributes to Parvimonas micra-induced bone resorption in diabetic rats with experimental periodontitis – Ying-Yi Chen – Molecular oral Microbiology

Non-Model Animal Microbiome

Microbiome depletion and recovery in the sea anemone, Exaiptasia diaphana, following antibiotic exposure – Sophie MacVittie – mSystems

Environmental Microbiome

Giant viral signatures on the Greenland ice sheet – Laura Perini – Microbiome

Photosynthetic carbon allocation in native and invasive salt marshes undergoing hydrological change: A mesocosm experiment – Ya-Lei Li – The Science of the Total Environment

Ibuprofen degradation by mixed bacterial consortia: metabolic pathway and microbial community analysis – A Rastogi – Chemosphere

Examining the impacts of salt specificity on freshwater microbial community and functional potential following salinization – Jonathon B Van Gray – Environmental Microbiology

Habitat conditions and not moss composition mediate microbial community structure in Swiss peatlands – Rachel Korn – Environmental Microbiology

May 17, 2024

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Today’s digest features bioinformatics binning methods, healthy dogs, lakes in South Africa, and more. For the human gut microbiome studies, check out the latest digest (May 15, 2024) by Grace Deitzler.

See you at #MVIF!

Skin microbiome

Intraspecies warfare restricts strain coexistence in human skin microbiomes – Christopher P. Mancuso – bioRxiv

Oral microbiome

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study – Memduh Bingöl – Journal of Clinical Periodontology

Urinary microbiome

Microbroth dilution method for antibiotic susceptibility testing of fastidious and anaerobic bacteria of the urinary microbiome – Wilson Geaman – Microbiology Spectrum

Respiratory tract

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease – Nick Quinn-Bohmann – BMC Biology

Food microbiome

Microbial community structure of plant-based meat alternatives – Franz-Ferdinand Rochn – pj Science of Food

Plan, root, soil

Functional team selection: a framework for local adaptation in plants and their belowground microbiomes – Nancy Collins Johnson and César Marín – ecoevoRxiv

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert – Patricio Arros – bioRxiv

Animal microbiome

Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial – Silke Salavati Schmitz – Access Microbiology

Early-life factors shaping the gut microbiota of Common buzzard nestlings – Hugo Pereira – Animal Microbiome

Animal experiment

13C-Stable isotope resolved metabolomics uncovers dynamic biochemical landscape of gut microbiome-host organ communications in mice – Xia Xiao – Microbiome

Water microbiome

Metagenomics datasets of water and sediments from eutrophication-impacted artificial lakes in South Africa – Grace Nkechinyere Ijoma – Scientific Data

Bioinformatics

Fairy: fast approximate coverage for multi-sample metagenomic binning – Jim Shaw and Yun William Yu – bioRxiv

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods – Daniel M Portik – biorXiv

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level – Amy S Graham – bioRxiv

Full factorial construction of synthetic microbial communities – Juan Diaz-Colunga – bioRxiv

ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences – Yao Pei – Microbiome

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

May 12, 2024

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Human and General Microbiome

Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota in vitro – Jenni Firrman – mBio

HIV rebound in HIV controllers is associated with a specific fecal microbiome profile – Yanhui Cai – European Journal of Immunology

Comparative analysis of the tumor microbiome, molecular profiles, and immune cell abundances by HPV status in mucosal head and neck cancers and their impact on survival – Rituraj Upadhyay – Cancer Biology & Therapy

Metatranscriptome and resistome of the endodontic microbiome – Ericka T Pinheiro – Journal of Endodontics

Microbiome of periodontitis and peri-implantitis before and after therapy: Long-read 16S rRNA gene amplicon sequencing – Pei-Shiuan Yu – Journal of Periodontal Research

Review: Akkermansia muciniphila: a deworming partner independent of type 2 immunity – Jiaqi Wang – Gut Microbes

Review: The gut microbiome in alcohol use disorder and alcohol-associated liver disease: A systematic review of clinical studies – Erica N Grodin – Alcohol, Clinical & Experimental Research

Review: Bile acid-microbiota crosstalk in hepatitis B virus infection – Jiaxin Wang – Journal of Gastroenterology and Hepatology

Review: Ecological insights into hematopoiesis regulation: unraveling the influence of gut microbiota – Kaiwen Zheng – Gut Microbes

Review: Interactions between host and gut microbiota in gestational diabetes mellitus and their impacts on offspring – Shuxian Wang – BMC Microbiology

Beneficial Microbes and Compounds

Review: Mechanisms of microbiota modulation: Implications for health, disease, and therapeutic interventions – Okechukwu Paul-Chima Ugwu – Medicine

Lactobacillus paracasei Jlus66 relieves DSS-induced ulcerative colitis in a murine model by maintaining intestinal barrier integrity, inhibiting inflammation, and improving intestinal microbiota structure – Fazheng Yu – European Journal of Nutrition

Conjugated linoleic acid metabolite impact in colorectal cancer: a potential microbiome-based precision nutrition approach – Adriana González – Nutrition Reviews

Microbiome in Animal Models

Aging amplifies a gut microbiota immunogenic signature linked to heightened inflammation – Maria Elisa Caetano-Silva – Aging Cell

Bacteroidota inhibit microglia clearance of amyloid-beta and promote plaque deposition in Alzheimer’s disease mouse models – Caroline Wasén – Nature Communications

Prevotella copri promotes vascular calcification via lipopolysaccharide through activation of NF-κB signaling pathway – Qing-Yun Hao – Gut Microbes

Non-Model Animal Microbiome

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

Characterizing the blood microbiota in healthy and febrile domestic cats via 16s rRNA sequencing – Liam Kitson – Scientific Reports

Plant/Rhizosphere Microbiome

Metagenomic sequencing and reconstruction of 82 microbial genomes from barley seed communities – Kalonji A Tshisekedi – Scientific Data

Modulation of rhizosphere microbial community and metabolites by bio-functionalized nanoscale silicon oxide alleviates cadmium-induced phytotoxicity in bayberry plants – Temoor Ahmed – The Science of the Total Environment

Phyllosphere fungal diversity generates pervasive nonadditive effects on plant performance – Brianna K Almeida – The New Phytologist

Environmental Microbiome

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities – Rehab Z Abdallah – mSystems

Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures – Wei Li – The ISME Journal

Genomic fingerprints of the world’s soil ecosystems – Emily B Graham – mSystems

Review: Insights into cyanobacterial blooms through the lens of omics – Ve Van Le – The Science of the Total Environment

Microbiome Analysis

fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data – Shen Zhang – Bioinformatics

Review: A Standard Pipeline for Analyzing the Endometrial Microbiome – Mychelle de Medeiros Garcia Torres – Reproductive Sciences 

May 8, 2024

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Happy Wednesday folks, we’re halfway through the week! Today’s blog features a number of interesting articles – it was difficult to pick just a few to highlight. Read on to learn about a new study that unveils the environment-specificity of secondary successional dynamics following microbiota disruption, a review summarizing the literature on how pesticide exposure affects the microbiota-gut-brain-axis, an investigation of how host phylogeny, diet, and anthropogenic factors shape the Cetacea gut microbiome – and more!

Human Microbiome

Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort – Tzipi Braun – Nature Communications

Improvements in Gut Microbiome Composition and Clinical Symptoms Following Familial Fecal Microbiota Transplantation in a Nineteen-Year-Old Adolescent With Severe Autism – Sabine Hazan – Journal of Medical Cases

[PREPRINT] Interplay between particle size and microbial ecology in the gut microbiome – Jeffrey Letourneau – bioRxiv

Shotgun metagenomic analysis of saliva microbiome suggests Mogibacterium as a factor associated with chronic bacterial osteomyelitis – Hiroko Yahara – PLOS One

[REVIEW] Pesticide exposure and the microbiota-gut-brain axis – Rie Matsuzaki – ISME Journal

Animal Experiments

Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks – Yuehui Hong – BMC Microbiome

Microbial Ecology

Synthesis of recovery patterns in microbial communities across environments – Stephanie D. Jurburg – BMC Microbiome

Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship – Johanna Vendermaesen – Ecology Letters

High speciation rate of niche specialists in hot springs – Qing He – ISME Journal

Plant, root, and soil microbiome

Effects of reduced snowpack due to climate warming on abiotic and biotic soil properties in alpine and boreal forest systems – Anastasiia Kosolapova – PLOS Climate

Microbiota recovery in a chronosquences of impoverished Cerrado soils with biosolids applications – Laibin Huang – Science of the Total Environment

Melatonin promotes the recovery of apple plants after waterlogging by shaping the structure and function of the rhizosphere microbiome – Yang Cao – Plant, Cell & Environment

Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils – Shengwei Liu – ISME Journal

Animal Microbiome

Antibiotic exposure alters the honeybee gut microbiota and may interfere with the honeybee behavioral caste transition – Zijing Zhang – Insect Science

Meta-analysis of the Cetacea gut microbiome: Diversity, co-evolution, and interaction with the anthropogenic pathobiome – Elena Radaelli – Science of the Total Environment

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification – Chandlar Tsz To Tsang – Molecular Ecology

Techniques & Methodology

A perfusion host-microbe bioreactor (HMB) system that captures dynamic interactions of secreted metabolites between epithelial cells cocultured with a human gut anaerobe – Jingyun Yang – Biotechnology and Bioengineering

Stable, fluorescent markers for tracking synthetic communities and assembly dynamics – Beatriz Jorrin – BMC Microbiome

Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations – Sonya R. Erlandson – BMC Environmental Microbiome

May 5, 2024

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Human and General Microbiome

Paternal microbiome perturbations impact offspring fitness – Ayele Argaw-Denboba – Nature

Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes – Chen Liao – Nature Microbiology

Human gut microbiota and their production of endocannabinoid-like mediators are directly affected by a dietary oil – Charlène Roussel – Gut Microbes

Leveraging genomic signatures of oral microbiome-associated antibiotic resistance genes for diagnosing pancreatic cancer – Xiaojing Shen – PloS ONE

Deciphering the Pancreatic Cancer Microbiome in Mainland China: Impact of Exiguobacterium/Bacillus ratio on Tumor Progression and Prognostic Significance – Zhengyan Zhang – Pharmacological Research

Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism – Xianyi Xiong – The ISME Journal

Microplastics and microbiota: Unraveling the hidden environmental challenge – Jean Demarquoy – World Journal of Gastroenterology

Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus – Emilene Da Silva Morais – Scientific Reports

Review: A catalog of ethanol-producing microbes in humans – Babacar Mbaye – Future Microbiology

Review: Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review – Madjid Morsli – Annals of Clinical Microbiology and Antimicrobials

Beneficial Microbes

A consortium of Hordeum vulgare and gut microbiota against non-alcoholic fatty liver disease via data-driven analysis – Su-Been Lee – Artificial Cells, Nanomedicine, and Biotechnology

Animal Microbiome

Amphibian tolerance to arsenic: microbiome-mediated insights – Isabella Ferreira Cordeiro – Scientific Reports

Combined effect of seasons and life history in an anuran strengthens the response and relationship between their physiology and gut microbiota – Jun-Kyu Park – Scientific Reports

Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments – Judith Guitart-Matas – Animal Microbiome

Effects of microbiome transplants on fly microbiome – Jorge Ferreira – Lab Animal

Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China – Hongjin Liu – Integrative Zoology

Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing – Edwin Omar Rivera-Lopez – Data in Brief

Plant Microbiome

Depletion of protective microbiota promotes the incidence of fruit disease – Xue Luo – The ISME Journal

Analysis of Salt Stress on Soil Microbial Community Composition and Its Correlation with Active Components in the Rhizosphere of Acanthopanax senticosus – Wenhui Yuan – Current Microbiology

Environmental Microbiome

Mechanisms and implications of bacterial-fungal competition for soil resources – Chaoqun Wang – The ISME Journal

Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments – Ye Chen – Microbiology Spectrum

Microbiome Analysis

mbDecoda: a debiased approach to compositional data analysis for microbiome surveys – Yuxuan Zong – Briefings in Bioinformatics

EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale – Sunil Nagpal – Microbiology Spectrum

mi-Mic: a novel multi-layer statistical test for microbiota-disease associations – Oshrit Shtossel – Genome Biology

Review: Unveiling microbial diversity: harnessing long-read sequencing technology – Daniel P Agustinho – Nature Methods

April 30, 2024

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Human microbiome

Safety and efficacy of faecal microbiota transplantation in patients with mild to moderate Parkinson’s disease (GUT-PARFECT): a double-blind, placebo-controlled, randomised, phase 2 trial – Anout Bruggeman – eClinicalMedicine

Implications of intestinal microecology and immune function alterations for immunotherapy outcomes in advanced unresectable lung adenocarcinoma – Shuang He – Clinical Respiratory Journal

Recipient microbiome-related features predicting metabolic improvement following fecal microbiota transplantation in adults with severe obesity and metabolic syndrome: a secondary analysis of a phase 2 clinical trial – Zhengxiao Zhang – Gut Microbes

Gut microbiome composition and metabolic activity in women with diverticulitis – Wenjie Ma – Nature Communications

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development – Raúl Y. Tito – Nature Medicine

Prediction and causal inference of hyperuricemia using gut microbiota – Yuna Miyajima – Scientific Reports

Early-life gut microbiota associates with allergic rhinitis during 13-year follow-up in a Finnish probiotic intervention cohort – Sampo Kallio – Microbiology Spectrum

Food microbiome

The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits – Elena A. Alexa – BMC Microbiome

Animal experiments

Sodium Propionate Oral Supplementation ameliorates Depressive-Like Behavior through Gut Microbiome and Histone 3 Epigenetic Regulation – Luiza Marques Prates Behrens – Journal of Nutritional Biochemistry

Colon impairments and inflammation driven by an altered gut microbiota leads to social behavior deficits rescued by hyaluronic acid and celecoxib – Oryan Agronyoni – BMC Medicine

Dissecting the respective roles of microbiota and host genetics in the susceptibility of Card9−/− mice to colitis – C. Danne – BMC Microbiome

Animal microbiome

Synergistic resistance of honeybee (Apis mellifera) and their gut microorganisms to fluvalinate stress – Jianhui Liu – Pesticide Biochemistry and Physiology

Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi) – Joel O. Abraham – Molecular Ecology

Water & extremophile microbiomes

Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench – Yan-Ru Dang – BMC Microbiome

Rhizospheric bacteria from the Atacama Desert hyper-arid core: cultured community dynamics and plant growth promotion – Juan Castro-Severyn – Microbiology Spectrum

Tools & techniques

Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols – Samuel P. Forry – Scientific Reports

Nanopore and Illumina sequencing reveal different viral populations from human gut samples – Ryan Cook – Microbial Genomics

April 28, 2024

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Human and General Microbiome

Genome Analysis of Epsilon CrAss-like Phages – Igor V Babkin – Viruses

Cervical microbiota dysbiosis associated with high-risk Human Papillomavirus infection – Natalia Zeber-Lubecka – PloS ONE

Association of the trimethylamine N-oxide with cardiovascular risk and vascular alterations in middle-aged patients with risk factors for cardiovascular diseases – Natalia Spasova – Bioscience Reports

Insights into microorganisms, associated factors, and the oral microbiome in infective endocarditis patients – Ayden Ismail – Frontiers in Oral Health

Alterations in the fecal microbiota of methamphetamine users with bad sleep quality during abstinence – Zijing Deng – BMC Psychiatry

Gut microbiome predicts cognitive function and depressive symptoms in late life – A Kolobaric – Molecular Psychiatry

Microbial signatures in human periodontal disease: a metatranscriptome meta-analysis – Armen Ovsepian – Frontiers in Microbiology

Gut microbiome composition reveals the distinctiveness between the Bengali people and the Indigenous ethnicities in Bangladesh – Ishtiaque Ahammad – Communications Biology

Comparative analysis of endometrial, vaginal, and gut microbiota in patients with and without adenomyosis – Marta Valdés-Bango – Acta Obstetricia et Gynecologica Scandinavica

Causal effect of gut microbiota and diabetic nephropathy: a Mendelian randomization study – Ganyuan He – Diabetology & Metabolic Syndrome

The characteristics of microbiome in the upper respiratory tract of COVID-19 patients – Xilong Zhang – BMC Microbiology

Review: Interplay of human gastrointestinal microbiota metabolites: Short-chain fatty acids and their correlation with Parkinson’s disease – Jiaji Liu – Medicine

Review: Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery – Saumitra Sengupta – Organic & Biomolecular Chemistry

Review: Oligella spp.: A systematic review on an uncommon urinary pathogen – Eric Farfour – European Journal of Clinical Microbiology & Infectious Diseases

Review: The potential importance of the built-environment microbiome and its impact on human health – Thomas C G Bosch – PNAS

Beneficial Microbes and Compounds

Vitamin D regulates microbiome-dependent cancer immunity – Evangelos Giampazolias – Science 

HMOs Impact the Gut Microbiome of Children and Adults Starting from Low Predicted Daily Doses – Danica Bajic – Metabolites

Effects of microbiome-based interventions on neurodegenerative diseases: a systematic review and meta-analysis – Zara Siu Wa Chui – Scientific Reports

A randomized, double-blinded, placebo-controlled clinical trial on Lactobacillus-containing cultured milk drink as adjuvant therapy for depression in irritable bowel syndrome – Marlynna Sarkawi – Scientific Reports

Animal Microbiome

Review: Understanding the Diversity and Roles of the Ruminal Microbiome – Gi Beom Keum – Journal of Microbiology

Plant Microbiome

Impacts of continuous cropping on the rhizospheric and endospheric microbial communities and root exudates of Astragalus mongholicus – Qin Zhou – BMC Plant Biology

Comparative analysis of root associated microbes in tropical cultivated and weedy rice (Oryza spp.) and temperate cultivated rice – Vani Juliyanti – Scientific Reports

Identifying causes and consequences of rhizosphere microbiome heritability – Maggie R Wagner – PLoS Biology

Environmental Microbiome

Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus ‘Igneacidithiobacillus’ – Dilanaz Arisan – Frontiers in Microbiology

Exploring changes in microplastic-associated bacterial communities with time, location, and polymer type in Liusha Bay, China – Ting Wang – Marine Environmental Research

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface – Jennifer L Goff – Environmental Microbiome

Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench – Yan-Ru Dang – Microbiome

Microbiome Analysis

Microbiome compositional data analysis for survival studies – Meritxell Pujolassos – NAR Genomics and Bioinformatics

Other

Periportal macrophages protect against commensal-driven liver inflammation – Yu Miyamoto – Nature

A case study to engage students in the research design and ethics of high-throughput metagenomics – Courtney Carroll Alexander – Journal of Microbiology & Biology Education