Category Archives: Human gut

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 10, 2023

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Last week’s highlights

Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial – Bertrand Routy – Nature Medicine

Top-down identification of keystone taxa in the microbiome – Guy Amit – Nature Communications

Sources of gut microbiota variation in a large longitudinal Finnish infant cohort – Roosa Jokela – EBioMedicine

Events

11th Microbiome R&D and Business Collaboration Forum and 5th Probiotics & Prebiotics Congress: USA – San Diego, CA – October, 19 – 20, 2023

Human and General Microbiome

Essay: A microbiome exercise – Christoph A Thaiss – Science

Mendelian randomisation analysis reveals the possible causal relationship between infections, microbiota and clinical disease – Shifang Li – Gut

Microbiome variance of the small bowel in Crohn’s disease – Lucas Wauters – Gut

Metagenomics analysis of the neonatal intestinal resistome – Stefano Leo – Frontiers in Pediatrics

Development of the intestinal microbiome in cystic fibrosis in early life – Courtney E Price – mSphere

Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease – Yogesh Singh – Molecular Neurodegeneration

Male-Biased Gut Microbiome and Metabolites Aggravate Colorectal Cancer Development – Ling Wang – Advanced Science

Review: Systematic review: Autism spectrum disorder and the gut microbiota – Jenni Korteniemi – Acta Psychiatrica Scandinavica

Review: Early-life respiratory infections and developmental immunity determine lifelong lung health – Clare M Lloyd – Nature Immunology

Microbiome and Evolution

Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life – Mia M Keady – PNAS

Shared evolutionary path in social microbiomes – Nelson Frazão – Molecular Biology and Evolution

Beneficial Microbes and Compounds

Review: Use of probiotics, prebiotics, and synbiotics in non-alcoholic fatty liver disease: A systematic review and meta-analysis – Lim Rong – Journal of Gastroenterology and Hepatology

Akkermansia muciniphila and Bifidobacterium bifidum Prevent NAFLD by Regulating FXR Expression and Gut Microbiota – Fulin Nian – Journal of Clinical and Translational Hepatology

Limosilactobacillus reuteri inhibits the acid tolerance response in oral bacteria – Gabriella Boisen – Biofilm

Animal Microbiome

Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome – Aravindh Nagarajan – Microbiome

Selection for environmental variance shifted the gut microbiome composition driving animal resilience – Cristina Casto-Rebollo – Microbiome

Plant Microbiome

Metabolic interaction models recapitulate leaf microbiota ecology – Martin Schäfer – Science

Environmental Microbiome

Microeukaryotic predators shape the wastewater microbiome – Nils Heck – Water Research

Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples – Cátia Santos-Pereira – Applied Microbiology and Biotechnology

Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes – Jeanett Daga-Quisbert – FEMS Microbiology Ecology

Built Environment

Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea – E Anders Kiledal – Microbiology Spectrum

Microbiome Research: Resources, Tools and Techniques

A catalog of bacterial reference genomes from cultivated human oral bacteria – Wenxi Li – NPJ Biofilms and Microbiomes

Gene-based microbiome representation enhances host phenotype classification – Thomas Deschênes – mSystems

Integrative meta-omics in Galaxy and beyond – Valerie C Schiml – Environmental Microbiome

Preprint: Compositional analysis of microbiome data using the linear decomposition model (LDM) – Yi-Juan Hu – bioRxiv

Preprint: Processing and Storage Methods Affect Oral and Gut Microbiome Composition – Dorothy K Superdock – bioRxiv

Preprint: A genome catalog of the early-life human skin microbiome – Zeyang Shen – bioRxiv

Review: In vitro models as a tool to study the role of gut microbiota in obesity – Abigail González – Critical Reviews in Food Science and Nutrition

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 16, 2023

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Thank you for answering my question above.

Today’s digest features indigenous chicken in Ethiopia, drug effects on gut microbiome, beach water microbial risk assessment, and more. See you at #MVIF next week!

Microbial ecology

Guild and Niche Determination Enable Targeted Alteration of the Microbiome – Oriane Moyne – bioRxiv

Genital microbiome

Interaction of genital microbiota in infertile couples – David Baud – bioRxiv

Gut microbiome

Emergence of community behaviors in the gut microbiota upon drug treatment – Sarela Garcia-Santamarina – bioRxiv

Skin microbiome

Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons – Marcus H. Y. Leung – Microbiome

Animal microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Laura Glendinning – bioRxiv

Animal experiments

Effects of fenbendazole on fecal microbiome in BPH/5 mice, a model of hypertension and obesity, a brief report – Kalie F. Beckers – Plos One

Gut microbiota and cognitive development in infant mice: Quantity and source of potable water – Chong-Su Kim and Dong-Mi Shin – Plos One

Plant microbiome

Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores – Eric W. Seabloom – Nature Communications

Methodology

Processing and Storage Methods Affect Oral and Gut Microbiome Composition – Dorothy K. Superdock – bioRxiv

QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification – Yu Yang – Water Research

Bioinformatics

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics – Rémi Gschwind – Nucleic Acids Research

June 13, 2023

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Today’s microbiome digest includes quite a few host-microbe studies, including one published by my colleague and highlighted below which focuses on the hindgut microbiome of the American cockroach.

Human gut microbiome

Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics – Hromada – and Venturelli – PLOS Biology

Construction of model animals to explore intestinal microbiome for detection of breast cancer – Ji et al. – PLOS One

Animal experiments

**Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics – Dukes et al. – Frontiers in Microbiology

Evaluation of microbial and vancomycin treatments in ulcerative colitis in murine models – Hasan and Yang – PLOS One

Animal microbiome

Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts – Hauer et al. – Microbiome

Insect phylogeny structures the bacterial communities in the microbiome of psyllids (Hemiptera: Psylloidea) in Aotearoa New Zealand – Martoni et al. – PLOS One

Water and extremophile microbiome

In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model – Park et al. – Microbiome

Phages and viruses

Beyond pathogenesis: Detecting the full spectrum of ecological interactions in the virosphere – Jurburg et al. – PLOS Biology

Phage therapy and the public: Increasing awareness essential to widespread use – McCammon et al. – PLOS One

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

May 16, 2023

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Happy Tuesday! Today’s microbiome digest is microbial ecology heavy, with articles focused on the gut microbiome, Antarctic endoliths’, water microbiomes, and more.

Human gut microbiome

Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer – Alexander et al. – Microbiome

Gut microbiome transitions across generations in different ethnicities in an urban setting—the HELIUS study – van der Vossen et al. – Microbiome

Water and extremophile microbiome

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability – Ettinger et al. – Microbiome

Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes – Vigneron et al. – Microbiome

preprint: Allochthonous groundwater microorganisms affect coastal seawater microbial abundance, activity and diversity – Yanuka-Golub et al. – bioRxiv

Built environment

preprint: Microbial Diversity on Ancestral Halls with Different Visitor Flow Rates Using Amplicon Sequencing – Liu et al. – bioRxiv

Techniques

Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies – Orellana et al. – Microbiome

May 12, 2023

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Today’s digest features studies on human respiratory tract, mouse models, bovine milk microbiome, and more. See you at #MVIF next week!

Respiratory tract microbiome

Review: Ecology of the respiratory tract microbiome – Ana Elena Pérez-Cobas – Trends in Microbiology

Cervicovaginal microbiome

The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by Lactobacillus iners regardless of HPV status – Daniela Vargas-Robles – bioRxiv

Gut microbiome

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic – Serena Porcari – Cell Host & Microbes

Profiling the human intestinal environment under physiological conditions – Dari Shalon – Nature

Interaction between gut microbiota and sex hormones and their relation to sexual dimorphism in metabolic diseases – Jose Antonio Santos-Marcos – Biology of Sex Differences

Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis – Paige Salerno – bioRxiv

Animal microbiome

Metagenomic analysis of milk microbiota in the bovine subclinical mastitis – Giulia Alessandri – bioRxiv

Animal experiments

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice – Paolo Manghi – Cell Reports

Bioinformatics

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning – Olga Mineeva – Plos Computational Biology

Technique

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing – David Calderón-Franco – Antonie van Leeuwenhoek

Built environment

The microbiome of an outpatient rehabilitation clinic and predictors of contamination: A pilot study – Gabriella Brigando – PlosOne