Author Archives: JP Cardenas

August 6, 2023

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Human and General Microbiome

Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota – Ming Ji – Nature Metabolism

Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer – Mohammed Muzamil Khan – Human Genomics

Metagenomics revealed a correlation of gut phageome with autism spectrum disorder – Khashayar Shahin – Gut Pathogens

The cervical microbiota of Hispanics living in Puerto Rico is nonoptimal regardless of HPV status – Daniela Vargas-Robles – mSystems

Illuminating the Oral Microbiome: Cellular Microbiology – Richard J Lamont – FEMS Microbiology Reviews

Meeting report of the sixth annual tri-service microbiome consortium symposium – Ida G Pantoja-Feliciano De Goodfellow – Environmental Microbiome

Evaluation of Intestinal Microbiota in Children With Sickle Cell Disease – Feryal Karahan – Journal of Pediatric Hematology/Oncology

Genetic and gut microbiome determinants of SCFA circulating and fecal levels, postprandial responses and links to chronic and acute inflammation – Ana Nogal – Gut Microbes

Review: Microbiota associated with peri-implantitis-A systematic review with meta-analyses – Érika B S Carvalho – Clinical Oral Implants Research

Review: Exploration of Gut Microbiome Research in Africa: A Scoping Review – Abdulkadir Yusif Maigoro – Journal of Medicinal Food

Animal Microbiome

Exploration of the candidate beneficial bacteria for P. vannamei culture by core microbiome analysis using amplicon sequencing – Natarajan Lalitha – Letters in Applied Microbiology

Plant Microbiome

A symbiotic footprint in the plant root microbiome – Kyle Hartman – Environmental Microbiome

Review: Towards integrative plant pathology – Tatiana Ruiz-Bedoya – Current Opinion in Plant Biology

More about the Microbes

Sodium levels and grazing pressure shape natural communities of the intracellular pathogen Legionella – Oded Bergman – Microbiome

Review: Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait – Maria Esteban-Torres – Gut Microbes

Microbiome Research: Resources, Tools and Techniques

ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization – Chen Yang – Bioinformatics

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

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 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 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