Tag Archives: animal models

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 23, 2023

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Highlights!

Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome – Mohammad H Mirhakkak – Nature Communications

Depletion of butyrate-producing microbes of the Firmicutes predicts nonresponse to FMT therapy in patients with recurrent Clostridium difficile infection – Hongliang Tian – Gut Microbes

Chagas disease is related to structural changes of the gut microbiota in adults with chronic infection (TRIPOBIOME Study) – José A Pérez-Molina – PLoS Neglected Tropical Diseases

Human and General Microbiome

Study of the gut microbiome in Egyptian patients with Parkinson’s Disease – Mohammad Mehanna – BMC Microbiology

Intestinal microbiota controls graft-versus-host disease independent of donor-host genetic disparity – Motoko Koyama – Immunity

A systematic review exploring the association between the human gut microbiota and brain connectivity in health and disease – Danique Mulder – Molecular Psychiatry

A macroecological perspective on genetic diversity in the human gut microbiome – William R Shoemaker – PloS One

Gut microbiota metabolites mediate the interplay between childhood maltreatment and psychopathology in patients with eating disorders – Giovanni Castellini – Scientific Reports

In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract – Yeon Bee Kim – Scientific Reports

Host microbiome-pathogen interactions in pediatric infections – Jillian H Hurst – Current Opinion in Infectious Diseases

Intratumoural microbiome can predict the prognosis of hepatocellular carcinoma after surgery – Lejia Sun – Clinical and Translational Medicine

A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis – Brett A McGregor – Parasites & Vectors

Microbiome-derived cobalamin and succinyl-CoA as biomarkers for improved screening of anal cancer – Sergio Serrano-Villar – Nature Medicine

Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease – Gemma L D’Adamo – Cell Reports. Medicine

Multimodal immune cell phenotyping in GI biopsies reveals microbiome-related T cell modulations in human GvHD – Sebastian Jarosch – Cell Reports. Medicine

Beneficial Microbes and Compounds

Prebiotics and the risk of upper digestive tract and stomach cancers: the PrebiotiCa study – Federica Turati – Journal of the Academy of Nutrition and Dietetics

Plant Microbiome

Disturbance of eucalypt forests alters the composition, function, and assembly of soil microbial communities – Ernest D Osburn – FEMS Microbiology Ecology

Reciprocal influence of soil, phyllosphere, and aphid microbiomes – Adrian Wolfgang – Environmental Microbiome

Review: Co-evolution within the plant holobiont drives host performance – Fantin Mesny – EMBO Reports

Environmental Microbiome

May microbial ecological baseline exist in continental groundwater? – Sining Zhong – Microbiome

Evolutionary patterns of archaea predominant in acidic environment – Rafael Bargiela – Environmental Microbiome

Microbiome Research: Resources, Tools and Techniques

Machine learning-based approaches for cancer prediction using microbiome data – Pedro Freitas – Scientific Reports

Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products – Maria Victoria Fernandez-Cantos – Frontiers in Microbiology

A bioinformatic analysis of zinc transporters in intestinal Lactobacillaceae – Uyen Huynh – Metallomics

Uncovering the Carboxylated Metabolome in Gut Microbiota-Host Co-metabolism: A Chemical Derivatization-Molecular Networking Approach – Yan-Zhen Wang – Analytical Chemistry

July 16, 2023

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Human and General Microbiome

A two-sample mendelian randomization analysis investigates associations between gut microbiota and infertility – Taozhi Li – Scientific Reports

Targeting gut microbiota-derived kynurenine to predict and protect the remodeling of the pressure-overloaded young heart – Bozhong Shi – Science Advances

Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma – Hong Wu – Cancer Research

Metabolic and inflammatory profiles, gut microbiota and lifestyle factors in overweight and normal weight young thai adults – Surasawadee Somnuk – PloS One

Metagenomic assessment of gut microbial communities and risk of severe COVID-19 – Long H Nguyen – Genome Medicine

Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics – Arianna Basile – Gut Microbes

Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer – Sadaf Najafi – BMC Microbiology

Aerobic exercise training and gut microbiome-associated metabolic shifts in women with overweight: a multi-omic study – Jukka E Hintikka – Scientific Reports

Glycogen availability and pH variation in a medium simulating vaginal fluid influence the growth of vaginal Lactobacillus species and Gardnerella vaginalis – Stephany Navarro – BMC Microbiology

Antibiotic-induced gut microbiota dysbiosis has a functional impact on purine metabolism – Xin Liu – BMC Microbiology

Coarse graining the human gut microbiome – Christian Diener – Cell Host & Microbe

Review: Intestinal mucus and their glycans: A habitat for thriving microbiota – Ana S Luis – Cell host & Microbe

Review: https://www.cell.com/trends/immunology/fulltext/S1471-4906(23)00111-4 – Isabel Tarrant – Trends in Immunology

Review: A comprehensive perspective on the interaction between gut microbiota and COVID-19 vaccines – Ming Hong – Gut Microbes

Beneficial Microbes and Compounds

Bacillus coagulans MZY531 alleviates intestinal mucosal injury in immunosuppressive mice via modulating intestinal barrier, inflammatory response, and gut microbiota – Zhongwei Zhao – Scientific Reports

Microbiome Engineering Using Probiotic Yeast: Saccharomyces boulardii and the Secreted Human Lysozyme Lead to Changes in the Gut Microbiome and Metabolome of Mice – Jungyeon Kim – Microbiology Spectrum

Animal Microbiome

Neotropical bee microbiomes point to a fragmented social core and strong species-level effects – Jordan G Kueneman – Microbiome

Multi-Omics Reveals the Impact of Exogenous Short-Chain Fatty Acid Infusion on Rumen Homeostasis: Insights into Crosstalk between the Microbiome and the Epithelium in a Goat Model – Yongkang Zhen – Microbiology Spectrum

Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats – Huasong Bai – Microbiology Spectrum

First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome – J Eduardo Martinez-Hernandez – PeerJ

Plant Microbiome

The predictive power of phylogeny on growth rates in soil bacterial communities – Jeth Walkup – ISME Communications

Potential relevance between soybean nitrogen uptake and rhizosphere prokaryotic communities under waterlogging stress – Tengxiang Lian – ISME Communications

Effects of nitrogen reduction combined with bio-organic fertilizer on soil bacterial community diversity of red raspberry orchard – Xu Yuan – PloS One

Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome – Wenke Smets – mBio

Environmental Microbiome

Pathogen resistance in soils associated with bacteriome network reconstruction through reductive soil disinfestation – Weijing Zhu – Applied Microbiology and Biotechnology

Microbiome Research: Resources, Tools and Techniques

Detection of Microorganisms in Body Fluid Samples – Xin Ji – Methods in Molecular Biology 

Guidelines for Microbiome Studies in Renal Physiology – Rikeish R Muralitharan – American Journal of Physiology. Renal Physiology

Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions – Thiyagarajan Gnanasekaran – mSystems

Review: Activity-based protein profiling in microbes and the gut microbiome – Lin Han – Current Opinion in Chemical Biology

July 3, 2023

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Human and General Microbiome

Bacterial Community Modifies Host Genetics Effect on Early Childhood Caries – F Blostein – Journal of Dental Research

Clostridioides difficile infection in infants: a case report and literature review – Zhirong Li – Gut Pathogens

The microbiota of pregnant women with SARS-CoV-2 and their infants – Heidi K Leftwich – Microbiome

Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles – James T Morton – Nature Neuroscience

Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet- and host-derived glycans – Mariana G Sartorio – PNAS

Site-specialization of human oral Gemella species – Julian Torres-Morales – Journal of oral Microbiology

Review: Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy – Andrew Maltez Thomas – Nature Reviews. Clinical Oncology

Review: Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics – Teija Ojala – Trends in Genetics

Review: Bacteria from the gut influence the host micronutrient status – Dorgeles Kouakou Dje Kouadio – Critical Reviews in Food Science and Nutrition

Beneficial Microbes and Compounds

Milk kefir alters fecal microbiota impacting gut and brain health in mice – Mariana de Fátima Albuquerque Pereira – Applied Microbiology and Biotechnology

Review: Calorie restriction mimetic drugs could favorably influence gut microbiota leading to lifespan extension – Tomoya Shintani – GeroScience

Are probiotics, prebiotics, and synbiotics beneficial in primary thyroid diseases? A systematic review with meta-analysis – Karolina Zawadzka – Annals of Agricultural and Environmental Medicine

Akkermansia muciniphila and Lactobacillus plantarum ameliorate systemic lupus erythematosus by possibly regulating immune response and remodeling gut microbiota – Mengchen Guo – mSphere

Effect of prebiotics, probiotics, synbiotics on depression: results from a meta-analysis – Qin Zhang – BMC Psychiatry

Animal Microbiome and Animal Model Microbiome

Patterns and determinants of the global herbivorous mycobiome – Casey H Meili – Nature Communications

Resistant starches from dietary pulses modulate the gut metabolome in association with microbiome in a humanized murine model of ageing – Saurabh Kadyan – Scientific Reports

The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats – Hanna Angstmann – Environmental Microbiome

Plant Microbiome

Different Techniques reveal the Difference of Community Structure and Function of Fungi from Root and Rhizosphere of Salvia miltiorrhiza Bunge – C Li – Plant Biology (Stuttgart, Germany)

Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth – Beatriz Lagunas – Microbiome

Core community drives phyllosphere bacterial diversity and function in multiple ecosystems – Ran Xue – The Science of the Total Environment

Environmental Microbiome

A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment – David Madrigal-Trejo – Microbial Ecology

Microbiome Research: Resources, Tools and Techniques

MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities – Billy Taj – Microbiome

Supervised learning and model analysis with compositional data – Shimeng Huang – PLoS Computational Biology

Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities – Qi Wang – Bioinformatics

Creation of a milk oligosaccharide database, MilkOligoDB, reveals common structural motifs and extensive diversity across mammals – Sierra D Durham – Scientific Reports

Review: Genetic Engineering of Resident Bacteria in the Gut Microbiome – Jack Arnold – Journal of Bacteriology

Review: Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA – Lin Yang – Nature Protocols

June 26, 2023

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Highlights!

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes – Matthew M Carter – Cell

A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression – Lauren E Davey – Nature Microbiology

The first international Rome consensus conference on gut microbiota and faecal microbiota transplantation in inflammatory bowel disease – Loris Riccardo Lopetuso – Gut

Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors – Julien Tap – Nature Communications

Human and General Microbiome

Key bacterial taxa determine longitudinal dynamics of aromatic amino acid catabolism in infants’ gut – Martin F Laursen – Gut Microbes

Low diversity microbiota and an increased metabolism of arginine and aromatic amino acids: a hallmark of hepatic encephalopathy in western Mexican patients with alcohol-associated cirrhosis – Tonatiuh Abimael Baltazar-Díaz – Journal of Applied Microbiology

Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy – Gang Fan – Gut Microbes

Species-Specific Analysis of Bacterial Vaginosis-Associated Bacteria – John Osei Sekyere – Microbiology Spectrum

Gut microbiota in nonalcoholic fatty liver disease: a PREDIMED-Plus trial sub analysis – Ana María Gómez-Pérez – Gut Microbes

Associations of Circulating Estrogens and Estrogen Metabolites with Fecal and Oral Microbiome in Postmenopausal Women in the Ghana Breast Health Study – Zeni Wu – Microbiology Spectrum

Meta-analysis of the effects of proton pump inhibitors on the human gut microbiota – Jiayi Zhang – BMC Microbiology

Animal Microbiome

Gut microbiomes of captive primates show phylosymbiosis, respond to dietary sugar reduction, and select for host-specific dietary microbes – Sally L Bornbusch – FEMS Microbiology Ecology

Environmental Microbiome

Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome – Xiaolan Lin – Microbiome

Microbiome Research: Resources, Tools and Techniques

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation – Dileep Kishore – mSystems

Human microbiome cultivation expands with AI – Marta Selma-Royo – Nature Biotechnology

GutBug: A Tool for Prediction of Human Gut Bacteria Mediated Biotransformation of Biotic and Xenobiotic Molecules Using Machine Learning – Aditya S Malwe – Journal of Molecular Biology

Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome – Céline Elie – Scientific Reports

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome – Elliot M Lee – mSystems

Assumptions on decision making and environment can yield multiple steady states in microbial community models – Axel Theorell – BMC Bioinformatics

EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies – Mayar Shahin – NPJ Systems Biology and Applications

Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy – Oshrit Shtossel – Gut Microbes

June 19, 2023

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Highlights!

A data-driven approach for predicting the impact of drugs on the human microbiome – Yadid M Algavi – Nature Communications

CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection – Lingdi Zhang – Microbiome

Human and General Microbiome

Gut and oral microbiome modulate molecular and clinical markers of schizophrenia-related symptoms: A transdiagnostic, multilevel pilot study – Jakleen J Lee – Psychiatry Research

Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: A blinded randomized controlled trial – Lepeng Zhou – Cell Host & Microbe

Metaproteomics Characterizes the Human Gingival Crevicular Fluid Microbiome Function in Periodontitis – Xiaolian Xiao – Journal of Proteome Research

Generation of dysbiotic microbiota in cutaneous leishmaniasis and enhancement of skin inflammation – Shumaila Naz – Microbial Pathogenesis

Oral microbiota may affect osteoradionecrosis following radiotherapy for head and neck cancer – Zhengrui Li – Journal of Translational Medicine

Oral microbial communities in 5-year-old children with versus without dental caries – Zhengyan Yang – BMC Oral Health

Analysis of gut microbiota in patients with Williams-Beuren Syndrome reveals dysbiosis linked to clinical manifestations – Federica Del Chierico – Scientific Reports

Review: Aspects of oral streptococcal metabolic diversity: Imagining the landscape beneath the fog – Peter Zuber – Molecular Microbiology

Review: Challenges and strategies for preventing intestinal damage associated to mercury dietary exposure – Pilar Rodríguez-Viso – Toxicology

Animal Microbiome

Phylogenetic comparative approach reveals evolutionary conservatism, ancestral composition, and integration of vertebrate gut microbiota – Benoît Perez-Lamarque – Molecular Biology and Evolution

Social transmission of bacterial symbionts homogenizes the microbiome within and across generations of group-living spiders – Clémence Rose – ISME Communications

Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation – Alexandra D Switzer – Environmental Microbiology

Microbiome Research Tools and Techniques

The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia – Jonas Schluter – Cell Host & Microbe

MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets – Matthys G Potgieter – PLoS Computational Biology

Methods for Analyzing the Gut Microbiota in Diabetic Retinopathy – Yinhua Huang – Methods in Molecular Biology

Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution – Atsufumi Ohta – Scientific Reports

June 12, 2023

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Highlights!

A microbiota-modulated checkpoint directs immunosuppressive intestinal T cells into cancers – Marine Fidelle – Science 

Using gut microbiota as a diagnostic tool for colorectal cancer: machine learning techniques reveal promising results – Fang Lu – Journal of Medical Microbiology

Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes – Joshua B R White – Nature

Human and General Microbiome

Skin maturation from birth to 10 years of age: Structure, function, composition and microbiome – Georgios N Stamatas – Experimental Dermatology

Ecological principles of fecal microbiota transplantation – Francisco Dini-Andreote – Trends in Microbiology

Human Genetics Influences Microbiome Composition Involved in Asthma Exacerbations despite Inhaled Corticosteroid Treatment – Javier Perez-Garcia – The Journal of Allergy and Clinical Immunology

Gut bacterial metabolism contributes to host global purine homeostasis – Kazuyuki Kasahara – Cell Host & Microbe

The relative abundance of fecal bacterial species belonging to the Firmicutes and Bacteroidetes phyla is related to plasma levels of bile acids in young adults – Francisco J Osuna-Prieto – Metabolomics

The effect of vitamin D supplementation on the gut microbiome in older Australians – Results from analyses of the D-Health Trial – Hai Pham – Gut Microbes

Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage – Howell Leung – NPJ Biofilms and Microbiomes

Gut microbiota dysbiosis promotes the development of epithelial ovarian cancer via regulating Hedgehog signaling pathway – Xinyue Hu – Gut Microbes

Preprint: Microbes with higher metabolic independence are enriched in human gut microbiomes under stress – Iva Veseli – bioRxiv

Review: Evolutionary implications of host genetic control for engineering beneficial microbiomes – Lucas P Henry – Current Opinion in Systems Biology

Review: It’s all relative: analyzing microbiome compositions, its significance, pathogenesis and microbiota derived biofilms: Challenges and opportunities for disease intervention – Sahar Zaidi – Archives of Microbiology

Animal Microbiome

Gut microbiome helps honeybee (Apis mellifera) resist the stress of toxic nectar plant (Bidens pilosa) exposure: Evidence for survival and immunity – Qihe Tang – Environmental Microbiology

Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha) – Javad Sadeghi – Molecular Ecology

The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts – Jinlong Li – Environmental Microbiome

Association analysis of gut microbiota-metabolites-neuroendocrine changes in male rats acute exposure to simulated altitude of 5500 m – Jianan Wang – Scientific Reports

Microbiomes of Blood-Feeding Triatomines in the Context of Their Predatory Relatives and the Environment – Hassan Tarabai – Microbiology Spectrum

Beneficial Microbes and Compounds

Probiotic interventions promote metabolic health in high fat-fed hamsters in association with gut microbiota and endocannabinoidome alterations – S Lacroix – Beneficial Microbes

Strains of Faecalibacterium prausnitzii and its extracts reduce blood glucose levels, percent HbA1c, and improve glucose tolerance without causing hypoglycemic side effects in diabetic and prediabetic mice – John Kallassy – BMJ Open Diabetes Research & Care

Effects of a low FODMAP diet on gut microbiota in individuals with treated celiac disease having persistent gastrointestinal symptoms – a randomized controlled trial – Anne Mari Herfindal – The British Journal of Nutrition

Designed α-sheet peptides disrupt uropathogenic E. coli biofilms rendering bacteria susceptible to antibiotics and immune cells – Alissa Bleem – Scientific Reports

Review: ‘Multi-omics’ data integration: applications in probiotics studies – Iliya Dauda Kwoji – NPJ Science of Food

Review: Micro-/bio-/nano-/syn-encapsulations and co-treatments of bioactive microbial feed supplementation in augmenting finfish health and aquaculture nutrition: a review – P Puri – Beneficial Microbes

Plant Microbiome

Taxonomic analysis reveals host preference of rare fungi in endophytes of Vitis vinifera from the Czech Republic – Miroslav Kolařík – Folia Microbiologica

Environmental Microbiome

Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities – Samuel E Miller – mSystems

Built Environment

A new approach of microbiome monitoring in the built environment: feasibility analysis of condensation capture – Jarrad T Hampton-Marcell – Microbiome

Microbiome Research Tools and Techniques

Preprint: A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset – Cankun Wang – bioRxiv

Preprint: DeepBiomarker2: Prediction of alcohol and substance use disorder risk in post-traumatic stress disorder patients using electronic medical records and multiple social determinants of health – Oshin Miranda – Research Square

Latent Dirichlet Allocation modeling of environmental microbiomes – Anastasiia Kim – PLoS Computational Biology

When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities – Sandra Dedrick – mSystems

June 5, 2023

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Human and General Microbiome

Altered gut microbiota as potential biomarker biomarkers for autism spectrum disorder in early childhood – Yingxin Zhao – Neuroscience

The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination – M Laura Rolon – Microbiome

Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort – Shantelle Claassen-Weitz – Microbiome

Secreted Akkermansia muciniphila threonyl-tRNA synthetase functions to monitor and modulate immune homeostasis – Su-Man Kim – Cell Host & Microbe

Gut Microbiome Composition is associated with future onset of Crohn’s Disease in Healthy First-Degree Relatives – Juan Antonio Raygoza Garay – Gastroenterology

Metagenome Investigation of Ocular Microbiota of Cataract Patients With and Without Type 2 Diabetes – Zheng Shao – Translational Vision Science & Technology

Longitudinal Gut Microbiota Dysbiosis Underlies Olanzapine-Induced Weight Gain – Li Qian – Microbiology Spectrum

Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut – Ida Ormaasen – BMC Genomics

Review: The Microbiome in Advanced Melanoma: Where Are We Now? – Dylan D Fortman – Current Oncology Reports

Review: Human gut microbiome: A primer for the clinician – Saurabh Kedia – JGH Open

Review: Role of gut microbiota and bacterial metabolites in mucins of colorectal cancer – Ming Gu – Frontiers in Cellular and Infection Microbiology

Beneficial Microbes and Compounds

Bacteriophage targeting microbiota alleviates non-alcoholic fatty liver disease induced by high alcohol-producing Klebsiella pneumoniae – Lin Gan – Nature Communications

Clostridium butyricum improves cognitive dysfunction in ICV-STZ-induced Alzheimer’s disease mice via suppressing TLR4 signaling pathway through the gut-brain axis – Yunfang Su – PloS One

Review: Regulation of gut microbiota by vitamin C, vitamin E and β-carotene – Xin-Yu Li – Food Research International

Animal Microbiome

Diversity of the Pacific Ocean coral reef microbiome – Pierre E Galand – Nature Communications

Effects of Aeromonas hydrophila infection on the intestinal microbiota, transcriptome, and metabolomic of common carp (Cyprinus carpio) – Lan Zhang – Fish & Shellfish Immunology

Genital tract microbiome dynamics are associated with time of Chlamydia infection in mice – Lihong Zhao – Scientific Reports

Environmental Microbiome

The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival – Benjamin J Wainwright – Environmental Microbiome

Microbiome Research Tools and Techniques

Formation and Analysis of Mono-species and Polymicrobial Oral Biofilms in Flow-Cell Models – Jessica Neilands – Methods in Molecular Biology

MAIRA: Protein-based Analysis of MinION Reads on a Laptop – Caner Bağcı – Methods in Molecular Biology 

Recovery and Analysis of Long-Read Metagenome-Assembled Genomes – Krithika Arumugam – Methods in Molecular Biology 

Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding – Marie-Pierre Chapuis – Molecular Ecology Resources

May 29, 2023

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Highlights!

Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains – Raymond Kiu – Nature Microbiology

Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach – Conor Feehily – Nature Communications

Human and General Microbiome

Expanding the repertoire of counterselection markers for markerless gene deletion in the human gut bacterium Phocaeicola vulgatus – André Neff – Anaerobe

Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection – Zheng Wang – Microbiome

Symbiotic microbiome Staphylococcus epidermidis restricts IL-33 production in allergic nasal epithelium via limiting the cellular necroptosis – Yung Jin Jeon – BMC Microbiology

Gut microbiome associated with low anterior resection syndrome after rectal cancer surgery – Min Jung Kim – Scientific Reports

Metabolomics Reveals Gut Microbiota Contribute to PPARα Deficiency-Induced Alcoholic Liver Injury – Ting Zhang – Journal of Proteome Research

Following your gut: the emerging role of the gut microbiota in predicting and treating immune-related adverse events – Antoine Desilets – Current Opinion in Oncology

Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma – Spyridon Megremis – Scientific Reports

The causal links between gut microbiota and COVID-19: A Mendelian randomization study – Jukun Song – Journal of Medical Virology

The Sexome – A proof of concept study into microbial transfer between heterosexual couples after sexual intercourse – Ruby Dixon – Forensic Science International

A systematic review of the protein composition of whole saliva in subjects with healthy periodontium compared with chronic periodontitis – Ana G Sánchez-Medrano – PloS ONE

Microbiome, Food and Diet

Metagenomic analysis and antibacterial activity of kefir microorganisms – Brianda D González-Orozco – Journal of Food Science

Fecal Metabolites as Biomarkers for Predicting Food Intake by Healthy Adults – Leila M Shinn – The Journal of Nutrition

More Microbes

Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota – Afaf Hamame – Scientific Reports

Animal Microbiome

Gut microbiome signatures of extreme environment adaption in Tibetan pig – Fangfang Zhao – NPJ Biofilms and Microbiomes

Holobiont Evolution: Population Theory for the Hologenome – Joan Roughgarden – The American Naturalist

Plant Microbiome

Integration of Phenotypes in Microbiome Networks for Designing Synthetic Communities: a Study of Mycobiomes in the Grafted Tomato System – Ravin Poudel – Applied and Environmental Microbiology

Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum – Jilu Che – Microbiology Spectrum

Bioinformatics, Microbiome Analysis and Techniques

MDM-Pred: a freely available web application for predicting the metabolism of drug-like compounds by the gut microbiota – A S Kolodnitsky – SAR and QSAR in Environmental Research

HONMF: integration analysis of multi-omics microbiome data via matrix factorization and hypergraph – Yuanyuan Ma – Bioinformatics 

Bayesian compositional regression with microbiome features via variational inference – Darren A V Scott – BMC Bioinformatics

The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae – Katherine M Elston – ISME Communications

Review: Unravelling animal-microbiota evolution on a chip – Ostaizka Aizpurua – Trends in Microbiology

May 22, 2023

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Have a nice day. Today we have a long list!

Highlights!

Airway dysbiosis accelerates lung function decline in chronic obstructive pulmonary disease – Weijie Liang – Cell Host & Microbe

An integrated tumor, immune and microbiome atlas of colon cancer – Jessica Roelands – Nature Medicine

General and Human Microbiome 

Skin microbiome alterations in upper extremity secondary lymphedema – Adana-Christine Campbell – PloS One

Isolation and identification of hyaluronan-degrading bacteria from Japanese fecal microbiota – Hazuki Akazawa – PloS One

Bacterial and metabolic phenotypes associated with inadequate response to ursodeoxycholic acid treatment in primary biliary cholangitis – Laura Martinez-Gili – Gut Microbes

Gut microbiota and its relation to inflammation in patients with bipolar depression: a cross-sectional study – Tingting Huang – Annals of General Psychiatry

Alterations in the Gut Microbiome and Metabolisms in Pregnancies with Fetal Growth Restriction – Zixin Tao – Microbiology Spectrum

16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients – Maartje Kristensen – Microbiology Spectrum

Single-Molecule Approach to 16S rRNA for Vaginal Microbiome Signatures in Response to Metronidazole Treatment – Hanyu Qin – Microbiology Spectrum

The presence of intratumoral Porphyromonas gingivalis correlates with a previously defined pancreatic adenocarcinoma, immune cell expression phenotype and with tumor resident, adaptive immune receptor features – Jacob C Kinskey – Carcinogenesis

Commentary: Microbiome is the key to preventing anastomotic leak in colorectal surgery – James M Kinross – Gut

Commentary: The aerobiome-health axis: a paradigm shift in bioaerosol thinking – Jake M Robinson – Trends in Microbiology

Review: Impact of the host microbiota on fungal infections: new possibilities for intervention? – Eve W L Chow – Advanced Drug Delivery Reviews

Review: Malnourished Microbes: Host-Microbiome Interactions in Child Undernutrition – Helen J Jones – Annual Review of Nutrition

Review: A narrative review from gut to lungs: non-small cell lung cancer and the gastrointestinal microbiome – Hely Shah – Translational Lung Cancer Research

Review: The interplay between oral microbiota, gut microbiota and systematic diseases – Xiujun Tan – Journal of Oral Microbiology

Animal Model Microbiome

Exposing new taxonomic variation with inflammation – a murine model-specific genome database for gut microbiome researchers – Ikaia Leleiwi – Microbiome

Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic – Huan Li – BMC Microbiology

Alterations of the gut microbiome and metabolic profile in CVB3-induced mice acute viral myocarditis – Qing Kong – BMC Microbiology

Seaweed polysaccharides treatment alleviates injury of inflammatory responses and gut barrier in LPS-induced mice – Yuanyuan He – Microbial Pathogenesis

Non-model Animal Microbiome

An entomopathogenic fungus exploits its host humoral antibacterial immunity to minimize bacterial competition in the hemolymph – Jia-Lin Wang – Microbiome

Engineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees – Haoyu Lang – Nature Communications

New insights into microbial and metabolite signatures of coral bleaching – Hao Sun – The Science of the Total Environment

Feeding hempseed cake alters the bovine gut, respiratory and reproductive microbiota – Thomas M Winders – Scientific Reports

Composition of mucus- and digesta-associated bacteria in growing pigs with and without diarrhea differed according to the presence of colonic inflammation – Farhad M Panah – BMC Microbiology

The microbiome and gene expression of honey bee workers are affected by a diet containing pollen substitutes – J Elijah Powell – PloS One

Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens – Xiang-Yu Wang – BMC Microbiology

Built Environment

Diversity and compositional differences of the airborne microbiome in a biophilic indoor environment – Akinobu Toyoda – Scientific Reports

Plant Microbiome

Review: Engineering the Crop Microbiota Through Host Genetics – Carmen Escudero-Martinez – Annual Review of Phytopathology

Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.) – Angélica Jara-Servin – PloS One

Microbiome Analysis

News: Long-read sequencing for the metagenomic analysis of microbiomes – Tristan Free – BioTechniques