Tag Archives: Microbiome research

September 11, 2023

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Human and General Microbiome

Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy – Jacobo de la Cuesta-Zuluaga – Gut Microbes

Elucidating the Role of the Microbiome in Ocular Diseases – Wendy Luo – The American Journal of Pathology

A binary module for microbiota-mediated regulation of γδ17 cells, hallmarked by microbiota-driven expression of programmed cell death protein 1 – Hsin-I Huang – Cell Reports

Resistant starch decreases intrahepatic triglycerides in patients with NAFLD via gut microbiome alterations – Yueqiong Ni – Cell Metabolism

Microbial signature of plaque and gut in acute coronary syndrome – Eugenia Pisano – Scientific Reports

Impact of the lipase inhibitor orlistat on the human gut microbiota – Yudai Uehira – Obesity Research & Clinical Practice

Metabolic network construction reveals probiotic-specific alterations in the metabolic activity of a synthetic small intestinal community – Jack Jansma – mSystems

Colonic phosphocholine is correlated with Candida tropicalis and promotes diarrhea and pathogen clearance – Xihong Zhou – NPJ Biofilms and Microbiomes

Differential dependence on microbiota of IL-23/IL-22-dependent gene expression between the small- and large-intestinal epithelia – Ayaka Nakatani – Genes to Cells

Identification of microbial markers associated with lung cancer based on multi-cohort 16 s rRNA analyses: A systematic review and meta-analysis – Wenjie Han – Cancer Medicine

Review: Targeting microbial quorum sensing: the next frontier to hinder bacterial driven gastrointestinal infections – Ying Su – Gut Microbes

Review: Illuminating the oral microbiome and its host interactions: recent Advancements in omics and bioinformatics technologies in the context of oral microbiome research – Jonathon L Baker – FEMS Microbiology Reviews

Review: Association between primary Sjögren’s syndrome and gut microbiota disruption: a systematic review and meta-analysis – Yue Shen – Clinical Rheumatology

Beneficial Microbes and Compounds

Washed microbiota transplantation for Clostridioides difficile infection: a national multi-center real-world study – Xia Wu – Journal of Digestive Diseases

Lactobacillus johnsonii N6.2 phospholipids induce immature-like dendritic cells with a migratory-regulatory-like transcriptional signature – Alexandra E Cuaycal – Gut Microbes

Akkermansia muciniphila supplementation prevents cognitive impairment in sleep-deprived mice by modulating microglial engulfment of synapses – Na Li – Gut Microbes

Food Microbiome

Metagenomics and metabolomics of Toddy, an Indian fermented date palm beverage – Souvik Das – Food Research International

Animal Microbiome

Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms – Viviani Mendes de Almeida – Gut Microbes

Ingestion and biodegradation of disposable surgical masks by yellow mealworms Tenebrio molitor larvae: Differences in mask layers and effects on the larval gut microbiome – Jiaming Wang – The Science of the Total Environment

Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers – Yu Wang – BMC Genomics

Microbiota-mediated competition between Drosophila species – Antoine Rombaut – Microbiome

Microbial signature profiles of Penaeus vannamei larvae in low-survival hatchery tanks affected by vibriosis – Guillermo Reyes – PeerJ

Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson’s disease – Kristopher J Schmit – Cell Reports

Plant Microbiome

Microbial communities associated with resin canal discoloration in mango fruit – Muhammad Umar – Letters in Applied Microbiology

Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana) – Daniel Bautista – Environmental Microbiology Reports

Environmental Microbiome

Antarctic snow algae: unraveling the processes underlying microbial community assembly during blooms formation – Daniela F Soto – Microbiome

Understanding how various forms of phosphorus stress affect microbiome functions and boost plant disease resistance: Insights from metagenomic analysis – Jie Kang – The Science of the Total Environment

Reductive soil disinfestation and Fe amendment improve soil microbial composition and Fritillaria production – Yue Yin – Applied Microbiology and Biotechnology

How Benthic Sediment Microbial Communities Respond to Glyphosate and Its Metabolite: a Microcosm Experiment – Christine M Cornish – Microbial Ecology

Functional conservation of microbial communities determines composition predictability in anaerobic digestion – Qiang Lin – The ISME Journal

Microbiome Research Tools

Development of an antibody fused with an antimicrobial peptide targeting Pseudomonas aeruginosa: A new approach to prevent and treat bacterial infections – Kenneth Johnson – PLoS Pathogens

Clustering microbiome data using mixtures of logistic normal multinomial models – Yuan Fang – Scientific Reports

A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria – Miguel Camacho-Sanchez – International Microbiology

Research Highlight: Microbiome screening platform finds drugs for bugs – Katie Kingwell – Nature Reviews. Drug Discovery

August 28, 2023

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Human and General Microbiome

The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia – Ana Elena Pérez-Cobas – Cell Reports. Medicine

A phenome-wide association study (PheWAS) to identify the health impacts of 4-cresol sulfate in the Nagahama Study – Huiting Ou – Scientific Reports

A meta-analysis of tissue microbial biomarkers for recurrence and metastasis in multiple cancer types – Xuebo Li – Journal of Medical Microbiology 

Microbe Profile: Ruminococcus gnavus: the yin and yang of human gut symbionts – Nathalie Juge – Microbiology

Oral Porphyromonas gingivalis infection affects intestinal microbiota and promotes atherosclerosis – Sowon Park – Journal of Clinical Periodontology

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study – Gertrude Ecklu-Mensah – Nature Communications

Very early life microbiome and metabolome correlates with primary vaccination variability in children – Michael Shaffer – mSystems

Carbohydrate quality, fecal microbiota and cardiometabolic health in older adults: a cohort study – Alessandro Atzeni – Gut Microbes

Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use – Udhghatri Kolli – Gut Microbes

The gut microbiota reprograms intestinal lipid metabolism through long noncoding RNA Snhg9 – Yuhao Wang – Science

Staphylococcus epidermidis activates keratinocyte cytokine expression and promotes skin inflammation through the production of phenol-soluble modulins – Michael R Williams – Cell Reports

Review: Targeting nonalcoholic fatty liver disease via gut microbiome-centered therapies – Mijra Koning – Gut Microbes

Review: Intracellular Fusobacterium nucleatum infection increases METTL3-mediated m6A methylation to promote the metastasis of esophageal squamous cell carcinoma – Songhe Guo – Journal of Advanced Research

Beneficial Microbes and Compounds

Characteristics of gut microbiota determine effects of specific probiotics strains in patients with functional constipation – Haohao Zhang – Chinese Medical Journal

Lacticaseibacillus rhamnosus TF318 prevents depressive behavior in rats by inhibiting HPA-axis hyperactivity and upregulating BDNF expression – Yujuan Zhao – Neuroscience Letters

Animal Model Microbiome

Role of mucin glycosylation in the gut microbiota-brain axis of core 3 O-glycan deficient mice – Erika Coletto – Scientific Reports

Non-Model Animal Microbiome

Outer membrane vesicles from a mosquito commensal mediate targeted killing of Plasmodium parasites via the phosphatidylcholine scavenging pathway – Han Gao – Nature Communications

Whole genome analyses of toxicants tolerance genes of Apis mellifera gut-derived Enterococcus faecium strains – Heba A H Zaghloul – BMC Genomics

Fungal Microbiome

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research – Julia M Kelliher – Microbiome

Plant Microbiome

Microbiome dataset of bacterial and fungal communities in anthosphere of twelve different wild plants in South Korea – Jihoon Kim – Data in Brief 

Environmental and Soil Microbiome

Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments – Xiaotian Zhou – Microbiome

Long-term agro-management strategies shape soil bacterial community structure in dryland wheat systems – Shikha Singh – Scientific Reports

Microbial community structure and functional prediction in five full-scale industrial park wastewater treatment plants – Tujun Tong – The Science of the Total Environment

Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum – Yuri Pinheiro Alves de Souza – Microbial Ecology

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole – Kai Sun – Microbiology Spectrum

A study of microbial diversity in a biofertilizer consortium – Cristóbal Hernández-Álvarez – PloS One

Microbiome Research: Resources, Tools and Techniques

Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data – Aubrey R Odom – Scientific Reports

Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution – Elisabetta Notario – Genes

A flexible quasi-likelihood model for microbiome abundance count data – Yiming Shi – Statistics in Medicine

Identification of multivariable Boolean patterns in microbiome and microbial gene composition data – George Golovko – Bio Systems

Machine learning classification by fitting amplicon sequences to existing OTUs – Courtney R Armour – mSphere

Review: Statistical normalization methods in microbiome data with application to microbiome cancer research – Yinglin Xia – Gut Microbes

Book Chapter: Elucidating the role of microbes in celiac disease through gnotobiotic modeling – Alberto Caminero – Methods in Cell Biology

August 20, 2023

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Highlights!

Human microbiome variation associated with race and ethnicity emerges as early as 3 months of age – Elizabeth K Mallott – PLoS Biology

Mapping the T cell repertoire to a complex gut bacterial community – Kazuki Nagashima – Nature

Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome – Liam H. Walsh – npj Science of Food 

High-resolution strain-level microbiome composition analysis from short reads – Herui Liao – Microbiome

Preprint: Profiling novel lateral gene transfer events in the human microbiome –  Tiffany Y. Hsu – bioRxiv

Human and General Microbiome

Preprint: Major data analysis errors invalidate cancer microbiome findings –  Abraham Gihawi – bioRxiv

Microdiversity of the vaginal microbiome is associated with preterm birth – Jingqiu Liao – Nature Communications

Dysbiosis of gut microbiota during fecal stream diversion in patients with colorectal cancer – Soo Young Lee – Gut Pathogens

The gut microbiome contributes to somatic morphine withdrawal behavior and implicates a TLR2 mediated mechanism – Bridget Truitt – Gut Microbes

Association of the human gut microbiota with vascular stiffness – Rafael R C Cuadrat – Scientific Reports

Gut microbiota and intervertebral disc degeneration: a bidirectional two-sample Mendelian randomization study – Ziming Geng – Journal of Orthopaedic Surgery and Research

News & Views: Microbiome alterations in autism spectrum disorder – Elena J Coley-O’Rourke – Nature Microbiology

Beneficial Microbes and Compounds

Rosmarinic acid alleviates intestinal inflammatory damage and inhibits endoplasmic reticulum stress and smooth muscle contraction abnormalities in intestinal tissues by regulating gut microbiota – Kan Li – Microbiology Spectrum

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline – Xiaolei Liu – Journal of Cachexia, Sarcopenia and Muscle

The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome – Carolina Baldisserotto Comerlato – Probiotics and Antimicrobial Proteins

Kombucha tea as an anti-hyperglycemic agent in humans with diabetes – a randomized controlled pilot investigation – Chagai Mendelson – Frontiers in Nutrition 

Animal Microbiome

The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host’s dietary adaption to bamboo – Feilong Deng – Microbiome

Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations – M McCauley – Nature Communications

Review: Toward an Integrated Understanding of the Lepidoptera Microbiome – Yongqi Shao – Annual Review of Entomology

Plant Microbiome

Characterization of bacterial community in tobacco leaves at flue-curing and redrying processing stages – Yue Yang – Scientific Reports

Environmental Microbiome

Inter-comparison of marine microbiome sampling protocols – Francisco Pascoal – ISME Communications

Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog – Adrien Vigneron – ISME Communications

Microbiome Research: Resources, Tools and Techniques

MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenome assembled genomes – Wanxin Li – PloS one

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J Pavia – Microbiome

Detection of viable commensal bacteria in murine melanoma tumors by culturomics – Catherine M Phelps – STAR Protocols

August 13, 2023

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Highlights!

Enterotypes of the human gut mycobiome – Senying Lai – Microbiome

Effect of butyrate-producing enterobacteria on advanced hepatocellular carcinoma treatment with atezolizumab and bevacizumab – Kazuhiro Nouso – Cancer Medicine

Parvimonas micra can translocate from the subgingival sulcus of the human oral cavity to colorectal adenocarcinoma – Kelly Conde-Pérez – Molecular Oncology

An Oral Microbial Biomarker for Early Detection of Recurrence of Oral Squamous Cell Carcinoma – Wei-Ni Lyu – ACS Infectious Diseases

Human and General Microbiome

Multilocus-sequence typing reveals clonality of Staphylococcus aureus in atopic dermatitis – Leszek Blicharz – Clinical and Experimental Dermatology

Metabarcoding approach to identify bacterial community profiling related to nosocomial infection and bacterial trafficking-routes in hospital environments – Bárbara Gimenes de Castro – Journal of Toxicology and Environmental Health. Part A

Identification of host gene-microbiome associations in colorectal cancer patients using mendelian randomization – Yaoxian Xiang – Journal of Translational Medicine

Bacterial amylases enable glycogen degradation by the vaginal microbiome – Dominick J Jenkins – Nature Microbiology

Babies, bugs and brains: How the early microbiome associates with infant brain and behavior development – Sebastian Hunter – PloS One

A retrospective analysis of vitamin B6 deficiency and associated changes of gut microbes in Crohn’s disease – Zhongsheng Feng – European Journal of Clinical Nutrition

The intestinal microbiota predicts COVID-19 severity and fatality regardless of hospital feeding method – Vanni Bucci – mSystems

Commentary and Views: The importance of the gut microbiome in the pathogenesis and transmission of SARS-CoV-2 – Carlo Brogna – Gut Microbes

Meta-analysis: Perturbations in gut microbiota composition in patients with polycystic ovary syndrome: a systematic review and meta-analysis – Pan Li – BMC Medicine

Letter: Caution regarding the specificities of pan-cancer microbial structure – Abraham Gihawi – Microbial Genomics

Review: Gut microbial beta-glucuronidase: a vital regulator in female estrogen metabolism – Shiwan Hu – Gut Microbes

Review: Three specific gut bacteria in the occurrence and development of colorectal cancer: a concerted effort – Dengmei Gong – PeerJ

Animal Microbiome (models and non-model organisms)

Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China – Michelle Baker – Nature Food

The enhancement in toxic potency of oxidized functionalized polyethylene-microplastics in mice gut and Caco-2 cells – Ji Wang – The Science of the Total Environment

Review: Geroprotective potential of microbiome modulators in the Caenorhabditis elegans model – Brandi C Miller – GeroScience

Microbiome Ecology and Evolution

Macroevolutionary constraints on global microbial diversity – Ford J Fishman – Ecology and Evolution

Evolutionary dynamics on sequential temporal networks – Anzhi Sheng – PLoS Computational Biology

Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community – Anna S Weiss – Nature Communications

Extremophiles

Earth to Mars: A Protocol for Characterizing Permafrost in the Context of Climate Change as an Analog for Extraplanetary Exploration – Kimberley R Miner – Astrobiology

Bioleaching of polymetallic sulphidic mining residues: influence of increasing solid concentration on microbial community dynamics and metal dissolution – Catherine Joulian – Research in Microbiology

Environmental Microbiome

Multidimensional specialization and generalization are pervasive in soil prokaryotes – Damian J Hernandez – Nature Ecology & Evolution

Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity – Brajogopal Samanta – Current Microbiology

Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study – Dámaris Núñez-Gómez – Environmental Microbiome

Opinion: New microbial tools to boost restoration and soil organic matters – Tadeo Sáez-Sandino – Microbial Biotechnology

Microbiome Research: Resources, Tools and Techniques

Optimization of fecal sample homogenization for untargeted metabolomics – Kieran Tarazona Carrillo – Metabolomics : Official Journal of the Metabolomic Society

metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering – Chunlin Hao – Microbiome

sccomp: Robust differential composition and variability analysis for single-cell data – Stefano Mangiola – PNAS

Metagenome sequencing and 103 microbial genomes from ballast water and sediments – Zhaozhao Xue – Scientific Data

July 30, 2023

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Human and General Microbiome

Resistome expansion in disease-associated human gut microbiomes – Simen Fredriksen – Microbiome

A microbial causal mediation analytic tool for health disparity and applications in body mass index – Chan Wang – Microbiome

Alterations of gut microbiota in biopsy-proven diabetic nephropathy and a long history of diabetes without kidney damage – Xiao Lu – Scientific Reports

Assessment of infant outgrowth of cow’s milk allergy in relation to the faecal microbiome and metaproteome – Diana M Hendrickx – Scientific Reports

Analysis of bacterial vaginosis, the vaginal microbiome, and sexually transmitted infections following the provision of menstrual cups in Kenyan schools: Results of a nested study within a cluster randomized controlled trial – Supriya D Mehta – PLoS Medicine

Evolutionary modeling suggests that addictions may be driven by competition-induced microbiome dysbiosis – Ohad Lewin-Epstein – Communications Biology

Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes – Kelsey N Thompson – Science Translational Medicine

Increased genital mucosal cytokines in Canadian women associate with higher antigen-presenting cells, inflammatory metabolites, epithelial barrier disruption, and the depletion of L. crispatus – Christina Farr Zuend – Microbiome

Insulin alleviates murine colitis through microbiome alterations and bile acid metabolism – Shuying He – Journal of Translational Medicine

The Vaginal Microbiota of Pregnant Women Varies with Gestational Age, Maternal Age, and Parity – Roberto Romero – Microbiology Spectrum

Unique microbial landscape in the human oropharynx during different types of acute respiratory tract infections – Hui Li – Microbiome

Systematic Review: Probiotics to prevent necrotising enterocolitis in very preterm or very low birth weight infants – Sahar Sharif – The Cochrane Database of Systematic Reviews

Comment: A gut feeling for drugs that have metabolic benefits – Eryun Zhang – Nature Communications

Review: Antibiotic perturbations to the gut microbiome – Skye R S Fishbein – Nature Reviews. Microbiology

Review: The global human gut microbiome: genes, lifestyles, and diet – Mona Parizadeh – Trends in Molecular Medicine

Beneficial Microbes and Compounds

5-Aminosalicylic acid alters the gut microbiota and altered microbiota transmitted vertically to offspring have protective effects against colitis – Haruka Wada – Scientific Reports

Food Microbiome

Presence of an ultra-small microbiome in fermented cabbages – Hae-Won Lee – PeerJ

Animal Microbiome

The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels – Simone Anzà – Microbiome

Early-life prophylactic antibiotic treatment disturbs the stability of the gut microbiota and increases susceptibility to H9N2 AIV in chicks – Xianghui Liang – Microbiome

Human-influenced diets affect the gut microbiome of wild baboons – Madelyn Moy – Scientific Reports

Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics – Barbara P Brito – Microbiome

Social network position is a major predictor of ant behavior, microbiota composition, and brain gene expression – Tomas Kay – PLoS Biology

Plant Microbiome

The root microbiome: techniques for exploration and agricultural applications – Ashling Cannon – BioTechniques

Environmental Microbiome

Recently-formed Antarctic lakes host less diverse benthic bacterial and diatom communities than their older counterparts – Jan Kollár – FEMS Microbiology Ecology

Microbiome Research: Resources, Tools and Techniques

Greengenes2 unifies microbial data in a single reference tree – Daniel McDonald – Nature Biotechnology

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning – Alex Chklovski – Nature Methods

Lectin-Seq: A method to profile lectin-microbe interactions in native communities – Robert L McPherson – Science Advances

A mixed-model approach for estimating drivers of microbiota community composition and differential taxonomic abundance – Amy R Sweeny – mSystems