September 24, 2022

Human and General Microbiome

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients – Thomas Vogl – Science Advances

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oluwaseun Rume-Abiola Oyewole – Microbiome

Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis – Victoria M Martin – Microbiome

Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism – Peter Spanogiannopoulos – Nature Microbiology

Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome – Rebecca C Simpson – Nature Medicine

Advances in the gut microbiome and mood disorders – Sabrina Mörkl – Current Opinion in Psychiatry

Review: Modulation of the intestinal microbiota impacts the efficacy of immunotherapy in cancer patients – A recent literature survey – Stella Ziegler – European Journal of Microbiology & Immunology

Animal Microbiome

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome – Tina Keller-Costa – Microbiome

Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis – Qian Zhou – Microbiome

Plant Microbiome

Response of soil microecology to different cropping practice under Bupleurum chinense cultivation – Li Liu – BMC Microbiology

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland – Jie Li – Microbiology Spectrum

Review: Investigating plant-microbe interactions within the root – Yuniar Devi Utami – Archives of Microbiology

Food Microbiome

Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation – Yuwei Tan – Microbiology Spectrum

More Microbes

A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis – Simon Mills – NPJ Biofilms and Microbiomes

Bioinformatics and Microbiome Analysis

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes – Lin Zhang – PLoS Computational Biology

September 10, 2022

Human and General Microbiome

Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life – Conner L Jackson – mBio

Gastrointestinal microbiota profile and clinical correlations in advanced EGFR-WT and EGFR-mutant non-small cell lung cancer – Woraseth Saifon – BMC Cancer

Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome – Anuradha Ravi – Communications Biology

Genetic Determinants of Hydrogen Sulfide Biosynthesis in Fusobacterium nucleatum Are Required for Bacterial Fitness, Antibiotic Sensitivity, and Virulence – Yi-Wei Chen – mBio

Preprint: Genomic and ecologic characteristics of the airway microbial-mucosal complex – Leah Cuthbertson – BioXriv 

Beneficial Microbes and Compounds

Lactiplantibacillus plantarum Regulated Intestinal Microbial Community and Cytokines to Inhibit Salmonella typhimurium Infection – Rui-Han Liu – Probiotics and Antimicrobial Proteins

Animal Microbiome

Exploration of rumen microbial and carbohydrate-active enzyme profiles in cattle fed coir a lignin-rich diet using a metagenomic approach – Munni Khatoon – Gene

Plant Microbiome

The core bacterial microbiome of banana (Musa spp.) – Henry W G Birt – Environmental Microbiome

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome – Yaping Guo – Environmental Microbiology

Environmental Microbiology

Virome analysis in lakes of the South Shetland Islands, Antarctica – 2020 – Tatiana Prado – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

Investigating differential abundance methods in microbiome data: A benchmark study – Marco Cappellato – PLoS Computational Biology

A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples – Ana Zúñiga – Frontiers in Bioengineering and Biotechnology

September 3, 2022

Highlights!!!

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome – Shuqin Zeng – Nature Communications → Authors presented and described the main features of the  Early-Life Gut Genomes (ELGG) catalog: a dataset of 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3-years old from different regions.

A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond – Brendon J Medley – The Journal of Biological Chemistry → AMUC_1438, a previously uncharacterized gene from A. muciniphila, encodes an O-glycopeptidase with mucin degrading capacity. This article shows relevant aspects of its enzymatic function. 

Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression – David Jose Delgado-Diaz – Microbiome → metaproteomic analysis on vaginal swab samples and transcriptomics analysis of cervicovaginal epithelial cell cultures showed that lactic acid, a commonly produced metabolite by the vaginal lactobacilli, is capable of enhancing genital epithelial barrier integrity; this microbial feature may help prevent invasion by sexually transmitted pathogens.

Human and General Microbiome

Review: A Perspective of the Urinary Microbiome in Lower Urinary Tract Infections – A Review – Rigoberto Pallares-Mendez – Current Urology Reports

Review: Methanogenic archaea in the human gastrointestinal tract – Christoph Hoegenauer – Nature Reviews. Gastroenterology & Hepatology

Meta-analysis of caries microbiome studies can improve upon disease prediction outcomes – Mark C Butcher – APMIS

Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure – Tatiana V Karpinets – BMC Cancer

Horizontal gene transfer enables programmable gene stability in synthetic microbiota – Teng Wang – Nature Chemical Biology

A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota – David M Versluis – mSystems

Gut microbiome dysbiosis is associated with increased mortality after solid organ transplantation – J Casper Swarte – Science Translational Medicine

Beneficial Microbes and Compounds

Intestinal Microbiomics and Metabolomics Insights into the Hepatoprotective Effects of Lactobacillus paracasei CCFM1222 Against the Acute Liver Injury in Mice – Weiling Guo – Probiotics and Antimicrobial Proteins

An Alternative Oat-Containing Ready-To-Use Therapeutic Food Does Not Alter Intestinal Permeability or the 16S rRNA Fecal Microbiome Configuration Among Children With Severe Malnutrition in Sierra Leone: A Randomized Controlled Trial – D Taylor Hendrixson – The Journal of Nutrition

Study on the Effect of Molecular Weight on the Gut Microbiota Fermentation Properties of Blackberry Polysaccharides In Vitro – Qiao-Yun Li – Journal of Agricultural and Food Chemistry

Animal Model Microbiome

Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition – Iman Zarei – Scientific Reports

Gut microbiota mediates the inhibition of lymphopoiesis in dietary-restricted mice by suppressing glycolysis – Si Tao – Gut Microbes

Non-Model Animal Microbiome

Limited microbiome differences in captive and semi-wild primate populations consuming similar diets – Sahana Kuthyar – FEMS Microbiology Ecology

Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome – Kathrin Busch – Nature Communications

Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts – Yujie Meng – Microbiome

Mucin O-glycan-microbiota axis orchestrates gut homeostasis in a diarrheal pig model – Bing Xia – Microbiome

Plant Microbiome

Stressful, isolated, yet diverse: Green roofs have rich microbiomes that are not dominated by oligotrophic taxa – Antoine Hénault – Environmental Microbiology Reports

Nodulation and nitrogen fixation in Medicago truncatula strongly alters the abundance of its root microbiota and subtly affects its structure – Andrzej Tkacz – Environmental Microbiology

Bioinformatic Tools and Microbiome Analysis Techniques

Gut bacterial nutrient preferences quantified in vivo – Xianfeng Zeng – Cell

Metric learning for comparing genomic data with triplet network – Zhi Ma – Briefings in Bioinformatics

STENSL: Microbial Source Tracking with ENvironment SeLection – Ulzee An – mSystems

Review: Emerging microfluidic technologies for microbiome research – Yue Yu – Frontiers in Microbiology

August 16, 2022

Human and General Microbiome

Crohn’s disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome – Jonathan P Jacobs – Genome Medicine

Preservation of fecal microbiome is associated with reduced severity of Graft-versus-Host Disease – Marina Burgos da Silva – Blood

Cobamide Sharing Is Predicted in the Human Skin Microbiome – Mary Hannah Swaney – mSystems

Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age – Maximilian J Bailey – Gut Microbes

Shotgun metagenomic sequencing reveals skin microbial variability from different facial sites – Qingzhen Wei – Frontiers in Microbiology

Review: Recent insights into the role of microbiome in the pathogenesis of obesity – Eduard W J van der Vossen – Therapeutic Advances in Gastroenterology

Model Animal Microbiome

Impact of habitual chewing on gut motility via microbiota transition – Fukie Yaoita – Scientific Reports

Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function – Alexandra Proctor – mSystems

Non-model Animal Microbiome

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate – David M Needham – Nature Microbiology

Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism – Sara Ricci – Scientific Reports

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts – Min Hui – PeerJ

Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure – Angela Zou – Microbiome

Environmental Microbiome

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction – Alessandro Rossi – Microbiome

Food Microbiome

Microbiome and Metabiotic Properties of Kefir Grains and Kefirs Based on Them –  Ding Fan – Microbiology

Profiling the role of microorganisms in quality improvement of the aged flue-cured tobacco – Xinying Wu – BMC Microbiology

August 6, 2022

Human and General Microbiome

The oral microbiome and lung cancer risk: An analysis of 3 prospective cohort studies – Emily Vogtmann – Journal of the National Cancer Institute

Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries – M J Carvalho – Nature Microbiology

Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer – Namjoo Kim – Scientific Reports

Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β-Lactam Resistome – Zhiguo Zhang – Environmental Science & Technology

Review: Porphyromonas gingivalis and dental stem cells crosstalk amplify inflammation and bone loss in the periodontitis niche – Devaraj Ezhilarasan – Journal of Cellular Physiology

Beneficial Microbes and Compounds

On the effect of flavonoids and dietary fibre in lingonberries on atherosclerotic plaques, lipid profiles and gut microbiota composition in Apoe(-/-) mice – Jiyun Liu – International Journal of food Sciences and Nutrition

The Gut-Brain-Microbiome Connection: Can Probiotics Decrease Anxiety and Depression? – Jennifer Maybee – Issues in Mental Health Nursing

The effect of Lactobacillus rhamnosus B10 on alcoholic liver injury and intestinal microbiota in alcohol-induced mice model – Xia Li – Journal of Food Biochemistry

Model Animal Microbiome

The effect of young blood plasma administration on gut microbiota in middle-aged rats – Taha Ceylani – Archives of Microbiology

Non-Model Animal Microbiome

Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus – Aleksandra I Krawczyk – Microbiome

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions – Manuel Aira – FEMS Microbiology Ecology

Ruminal Microbiota Determines the High-Fiber Utilization of Ruminants: Evidence from the Ruminal Microbiota Transplant – Xiaodong Chen – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

Computational approach to modeling microbiome landscapes associated with chronic human disease progression – Lu Li – PLoS Computational Biology

Guideline for the analysis of the microbial communities of the human upper airways – Leonardo Mancabelli – Journal of Oral Microbiology

March 1, 2022

General microbiome

Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analyses – Ramaloko et al. – Environmental Microbiology

Global diversity and distribution of mushroom-inhabiting bacteria – Gohar et al. – Environmental Microbiology Reports

Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on blaNDM Transmission – Dong et al. – Microbiology Spectrum

Multi-site human microbiome

Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis – Cai et al. – Microbiology Spectrum

Human respiratory microbiome

Early life inter-kingdom interactions shape the immunological environment of the airways – C Pattaroni et al. – Microbiome

Human gut microbiome

Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers – Coker et al. – Microbiome

Animal experiments

Development of a rational framework for the therapeutic efficacy of fecal microbiota transplantation for calf diarrhea treatment – Islam et al. – Microbiome

Animal microbiome

Comparative microbiome analysis of Diaphorina citri and its associated parasitoids Tamarixia radiata and Diaphorencyrtus aligarhensis reveals Wolbachia as a dominant endosymbiont – Ashraf et al. – Environmental Microbiology

Plant, root, and soil microbiome

Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured – Kajihara et al. – New Phytologist

Embracing mountain microbiome and ecosystem functions under global change –  Wang et al. – New Phytologist

Nitrogen fertilization disrupts the temporal dynamics of arbuscular mycorrhizal fungal hyphae but not spore density and community composition in a wheat field – Babalola et al. – New Phytologist

Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain – Pang et al. – Microbiology Spectrum

Seed microbiota revealed by a large-scale meta-analysis including 50 plant species – Simonin et al. – New Phytologist

Viewpoint: Plant–microbe eco-evolutionary dynamics in a changing world – Angulo et al. – New Phytologist

Stem traits, compartments, and tree species affect fungal communities on decaying wood – Yang et al. – Environmental Microbiology

Microplastics reduce soil microbial network complexity and ecological deterministic selection – Shi et al. – Environmental Microbiology

The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA – Rolando et al. – Microbiome

Water and extremophile

“Boom-and-busted-dynamics” of phytoplankton-virus interactions explain the paradox of the plankton – Flynn et al. – New Phytologist

Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts – Taylor et al. – Environmental Microbiology

Global 16S rRNA diversity of provannid snail endosymbionts from Indo-Pacific deep-sea hydrothermal vents – Breusing et al. – Environmental Microbiology Reports

Sources of protein diet differentially stimulate the gut and water microbiota under freshwater crayfish, marron (Cherax cainii, Austin 2002) culture – Foysal et al. – Environmental Microbiology Reports

December 17, 2021

Human and General Microbiome

Association of microbial dynamics with urinary estrogens and estrogen metabolites in patients with endometriosis – Nhung Le – PloS ONE

Gut Microbiome in Probable Intestinal Tuberculosis and Changes following Anti-Tuberculosis Treatment – Hyuk Yoon – Yonsei Medical Journal

Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis – Tomohiro Hayashi – Frontiers in Cardiovascular Medicine

Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community – Yongyong Kang – Microbiology Spectrum

Stability of healthy subgingival microbiome across space and time – Ryan Tamashiro – Scientific Reports

Successional Stages in Infant Gut Microbiota Maturation – Leen Beller – mBio

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Peng Zhang – The ISME Journal

Bacterial vaginosis and health-associated bacteria modulate the immunometabolic landscape in 3D model of human cervix – Paweł Łaniewski – NPJ Biofilms and Microbiomes

Acute malnutrition and its determinants of preschool children in Bangladesh: gender differentiation – Md Reazul Karim – BMC Pediatrics

SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts – M Nazmul Hoque – Scientific Reports

Gut Mycobiota Dysbiosis in Pulmonary Tuberculosis Patients Undergoing Anti-Tuberculosis Treatment – Demin Cao – Microbiology Spectrum

Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid – Michael E J Buhl – International Journal of Systematic and Evolutionary Microbiology

Human and General Microbiome – Reviews

Review: The Role of Gut Microbiota and Genetic Susceptibility in the Pathogenesis of Pancreatitis – Fumin Xu – Gut and Liver

Review: Transcript host-RNA signatures to discriminate bacterial and viral infections in febrile children – Danilo Buonsenso – Pediatric Research

Review: The role of anaerobic bacteria in the development and prevention of colorectal cancer: A review study – Mehrdad Mohammadi – Anaerobe

Review: Lung microbiome, gut-lung axis and chronic obstructive pulmonary disease – Kuppan Gokulan – Current Opinion in Pulmonary Medicine

Systematic review: Gut microbiota modulation as a possible mediating mechanism for fasting-induced alleviation of metabolic complications: a systematic review – Pooneh Angoorani – Nutrition & Metabolism

Systematic review: The relation between the gut microbiome and osteoarthritis: A systematic review of literature – Emanuele Chisari – PloS ONE

Outlook: Ovarian cancer and the microbiome: a complex relationship – Julianna Photopoulos – Nature

Beneficial Microbes and Compounds

Oligofructose-enriched inulin intake, gut microbiome characteristics and the V̇O2peak response to high-intensity interval training in healthy inactive adults – Camilla J Williams – The Journal of Nutrition

Lactiplantibacillus plantarum DMDL 9010 alleviates dextran sodium sulfate (DSS)-induced colitis and behavioral disorders by facilitating microbiota-gut-brain axis balance – Yan-Yan Huang – Food & Function

Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial – Dorit Vedel Ankersen – Journal of Medical Internet Research

Effect of dietary selenium intake on gut microbiota in older population in Enshi region – Zi-Xiong Zhang – Genes and Environment

Animal Microbiome

The bacterial biome of ticks and their wildlife hosts at the urban-wildland interface – Siobhon L Egan – Microbial Genomics

The gut microbiota of wild wintering great bustard (Otis tarda dybowskii): survey data from two consecutive years – Zhiyuan Lu – PeerJ

You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches – Melissa R Ingala – Animal Microbiome

Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level – Rupert Mazzucco – Proceedings of the Royal Society B. Biological Sciences

Plant and Fungi Microbiome

The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host – Maria J Soto-Giron – Scientific Reports

Autotoxin Rg(1) Induces Degradation of Root Cell Walls and Aggravates Root Rot by Modifying the Rhizospheric Microbiome – Yanguo Xu – Microbiology Spectrum

Multitrophic Interactions Between Arbuscular Mycorrhizal Fungi, Foliar Endophytic Fungi and Aphids – Nadia Ab Razak – Microbial Ecology

Other Microbes

Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia – Anna G Burrichter – BMC Microbiology

Methods

Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes – Angie Mordant – Microbiology Spectrum

Sample Processing for Metaproteomic Analysis of Human Gut Microbiota – Carmen García-Durán – Methods in Molecular Biology Enhancing Microbiome Research through Genome-Scale Metabolic Modeling – Nana Y D Ankrah – mSystems

July 24, 2021

Have a nice weekend! Today in this Digest, we have a set of papers covering different aspects of the human microbiome in health and disease. For example, connections between gut microbiota and different clinical parameters in patients with inflammatory bowel disease, and another study showing a relationship between TMAO and heart damage.  

Human and General Microbiome

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease – Jonathan Wei Jie Lee – Cell Host & Microbe

Gut Microbiota-generated Metabolite, Trimethylamine-N-oxide, And Subclinical myocardial damage: a multicenter study from Thailand – Vichai Senthong – Scientific Reports

Association Between The Urogenital Microbiome And Surgical Treatment Response In Women Undergoing Mid-urethral Sling Surgery for Mixed Urinary Incontinence – Holly E Richter – American Journal Of Obstetrics And Gynecology

Review: Personalized Approach To Childhood Obesity: Lessons From Gut Microbiota And Omics studies. Narrative review and insights from the 29th European childhood obesity congress – Aneta Gawlik – Pediatric Obesity

Review: The complex interplay of gut microbiota with the five most common cancer types: from carcinogenesis to therapeutics to prognosis – Kayla Jaye – Critical Reviews In Oncology/hematology

Clostridium culturomicium sp. nov. and Clostridium jeddahitimonense sp. nov., Novel members of the Clostridium genus isolated from the stool of an obese Saudi Arabian. – Hoang Thong Kieu – Current Microbiology

Effect Of Intestinal Microbiota Imbalance Associated With Chronic Hepatitis B Virus infection on the expression of microRNA‑192 and GLP‑1 – Yinghui Liu – Molecular Medicine Reports

Variations In The Oral Microbiome Are Associated With Depression In Young Adults – Benjamin Wingfield – Scientific Reports

Comparative Analysis Of The Bronchoalveolar Microbiome In Portuguese Patients With different chronic lung disorders – Susana Seixas – Scientific Reports

Microbiome and COVID19

Review: Recent Advance Of ACE2 And Microbiota Dysfunction In COVID-19 Pathogenesis – Zhidan Yu – Heliyon

Animal Microbiome

Review: T Cell Subsets And Environmental Factors In Citrobacter rodentium Infection – Brigitta Stockinger – Current Opinion In Microbiology

Chitinibacter bivalviorum sp. nov., Isolated From The Gut Of The Freshwater Mussel Anodonta arcaeformis – Jee-Won Choi – International Journal Of Systematic And Evolutionary Microbiology

Beneficial Microbes and Compounds

Nanocapsule-mediated Sustained H2 Release In The Gut Ameliorates Metabolic dysfunction-associated fatty liver disease – Zhaokui Jin – Biomaterials

Aryl Hydrocarbon Receptor Activation By Lactobacillus reuteri Tryptophan Metabolism alleviates Escherichia coli-induced mastitis in mice – Caijun Zhao – PLoS Pathogens

Grape Seed Proanthocyanidins Reduced The Overweight Of C57BL/6J Mice through modulating adipose thermogenesis and gut microbiota. – Haiping Du – Food & Function

Plant Microbiome

Distribution Of The Potential Pathogenic Alternaria On Plant Leaves Determines foliar fungal communities around the disease spot – Jiemeng Tao – Environmental Research

Prolonged Drought Imparts Lasting Compositional Changes To The Rice Root Microbiome – Christian Santos-Medellín – Nature Plants

News & Views: Drought Dampens Microbiome Development – Yi Song – Nature Plants

Built Environment

Factors Associated With Elevated Levels Of Antibiotic Resistance Genes In Sewer sediments and wastewater – Eramo Alessia – Environmental Science

Microbiome Techniques and Analysis

A Novel, Scalable, And Modular Bioreactor Design For Dynamic Simulation Of The digestive tract – Salam Habib – Biotechnology And Bioengineering

Assessment Of Biolog Ecoplate(TM) Method For Functional Metabolic Diversity Of aerotolerant pig fecal microbiota – A Checcucci – Applied Microbiology And Biotechnology

Structural Identifiability Of The Generalized Lotka-Volterra Model For Microbiome studies – Christopher H Remien – Royal Society Open Science

Validation Of The MYChrOme™ Culture Plate For Detection And Differentiation Of Rapid-Growing Nontuberculous Mycobacteria in potable and non-potable water: AOAC  Performance Tested MethodSM 062101 – Katherine E Fisher – Journal Of AOAC International

July 22, 2021

Human and General Microbiome

The Change Of Gut Microbiota In MDD Patients Under SSRIs Treatment – Yang Shen – Scientific Reports

Minimal-moderate Variation Of Human Oral Virome And Microbiome In IgA Deficiency – Maria José de la Cruz Peña – Scientific Reports

Weight Shapes The Intestinal Microbiome In Preterm Infants: Results Of A Prospective observational study – Fardou H Heida – BMC Microbiology

Functional Heterogeneity In The Fermentation Capabilities Of The Healthy Human Gut microbiota – Thomas Gurry – PloS One

Characterization Of The Blood And Neutrophil-specific Microbiomes And Exploration Of potential bacterial biomarkers for sepsis in surgical patients – Chenyang Wang – Immunity, Inflammation And Disease

Cognitive Function Improvement After Fecal Microbiota Transplantation In In Alzheimer’s dementia patient: a case report – Soo-Hyun Park – Current Medical Research And Opinion

Amplicon And Metagenomic Analysis Of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS – Waleed Aljabr – mSphere

Dental Plaque Microbial Resistomes Of Periodontal Health And Disease And Their Changes after Scaling and Root Planing Therapy – Yutong Kang – mSphere

Archaea Are Rare And Uncommon Members Of The Mammalian Skin Microbiome – Alexander K Umbach – mSystems

Association Between Human Genetic Variants And The Vaginal Bacteriome Of Pregnant Women – Wei Fan – mSystems

Population-wide Diversity And Stability Of Serum Antibody Epitope Repertoires against human microbiota – Thomas Vogl – Nature Medicine

Dynamic Colonization Of Microbes And Their Functions After Fecal Microbiota Transplantation for Inflammatory Bowel Disease – Nathaniel D Chu – mBio

Review: Tryptophan Metabolites Modulate Inflammatory Bowel Disease And Colorectal Cancer By affecting immune system – Moein Ala – International Reviews Of Immunology

Review: From Gut Microbiota To Host Appetite: Gut Microbiota-derived Metabolites As Key regulators – Hui Han – Microbiome

The Roles Of Cytoplasmic Lipid Droplets In Modulating Intestinal Uptake Of Dietary Fat – Alyssa S Zembroski – Annual Reviews Of Nutrition

Review: Intestinal Microbiota In The SARS-CoV-2 Infection: What Is Known? – Patrícia Brito Rodrigues – Advances In Experimental Medicine And Biology

Review: The Microbiota-Gut-Brain Axis And Epilepsy – Qiang Yue – Cellular And Molecular Neurobiology

In Brief: Microbiota Links To Immunotherapy Toxicity – Sarah Seton-Rogers – Nature Reviews Cancer

Opinion: Forming Consensus To Advance Urobiome Research – Linda Brubaker – mSystems

Beneficial Microbes and Compounds

A High-protein Diet Containing Inulin/oligofructose Supports Body Weight Gain associated with lower energy expenditure and carbohydrate oxidation, and alters faecal microbiota in C57BL/6 mice – Franziska Koch – Journal Of Nutritional Science

Immunosuppressive Activity Is Attenuated By Astragalus polysaccharides Via remodeling the gut microenvironment in melanoma mice – Guiqing Ding – Cancer Science

Review: The Interaction Effect Between Tea Polyphenols And Intestinal Microbiota: Role In ameliorating neurological diseases – Mengyu Hong – Journal Of Food Biochemistry

Review: Nutritional Interventions And The Gut Microbiome In Children – Saurabh Mehta – Annual Reviews Of Nutrition

Animal Microbiome and Animal Models

Interspecific Variation And Functional Traits Of The Gut Microbiome In Spiders From the wild: The largest effort so far. – Kaomud Tyagi – PloS One

Vibrio vulnificus Induces The Death Of A Major Bacterial Species In The Mouse Gut via cyclo-Phe-Pro. – Jeong-A Kim – Microbiome

Maternal Cecal Microbiota Transfer Rescues Early-life Antibiotic-induced Enhancement of type 1 diabetes in mice. – Xue-Song Zhang – Cell Host & Microbe

Comprehensive Cultivation Of The Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs. – Xiaofan Wang – mSystems

Plant Microbiome

Drought Stress And Plant Ecotype Drive Microbiome Recruitment In Switchgrass – Tie-Yuan Liu – Journal Of Integrative Plant Biology

Microbe-dependent Heterosis In Maize – Maggie R Wagner – Proceedings Of The National Academy Of Sciences Of The United States Of America

Review: Prioritizing Host Phenotype To Understand Microbiome Heritability In Plants – Maggie R Wagner – The New Phytologist

Microbiome Analysis and Techniques

On The Robustness Of Inference Of Association With The Gut Microbiota In Stool, rectal swab and mucosal tissue samples – Shan Sun – Scientific Reports

Amplicon Sequence Variants Artificially Split Bacterial Genomes Into Separate Clusters. – Patrick D Schloss – MSphere

Linking Plasmid-based Beta-lactamases To Their Bacterial Hosts Using Single-cell fusion PCR – Peter J Diebold – eLife

An Integrated Machine Learning Framework For A Discriminative Analysis Of schizophrenia using multi-biological data. – Peng-Fei Ke – Scientific Reports

An Intestinal Gut Organ Culture System For Analyzing Host-Microbiota Interactions – Shalhevet Azriel – Journal Of Visualized Experiments (JoVE)

Mycobiome (Early 2021 Semi-Annual Fungal Microbiome Picks)

It’s been a while, but its time to highlight some recent mycobiome articles!

Human mycobiome

Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities – Wu et al. – Microbiome

Gut mycobiota in immunity and inflammatory disease – Li et al. – Immunity

Response to fungal dysbiosis by gut-resident CX3CR1(+) mononuclear phagocytes aggravates allergic airway disease.- Li et al. – Cell Host Microbe. 

Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans. – Bacher et al. – Cell. 

Prevalence and diversity of filamentous fungi in the airways of cystic fibrosis patients – a Dutch, multicentre study. – Engle et al. – J Cyst Fibros.

Early gut mycobiota and mother-offspring transfer. – Schei – Microbiome

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age. – Willis et al – FASEB J.

Investigating colonization of the healthy adult gastrointestinal tract by fungi. – Auchtung et al. – mSphere.

CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi. – Leonardi et al. – Science.

Commensal Candida albicans positively calibrates systemic Th17 immunological responses. – Shao et al – Cell Host Microbe. 

Macrophages maintain epithelium integrity by limiting fungal product absorption. – Chikina et al. – Cell.

Fungal symbionts produce prostaglandin E2 to promote their intestinal colonization. – Tan et al. – Front Cell Infect Microbiol.

The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. – Aykut et al – Nature. 

Fungal microbiota dysbiosis in IBD. – Sokol et al – Gut.

Malassezia is associated with Crohn’s disease and exacerbates colitis in mouse models. – Limon et al – Cell Host Microbe.

Macrophage interactions with fungi and bacteria in inflammatory bowel disease. – Leonardi et al. – Curr Opin Gastroenterol.

Fungi participate in the dysbiosis of gut microbiota in patients with primary sclerosing cholangitis. – Lemoinne et al – Gut

Intestinal fungi contribute to development of alcoholic liver disease. – Yang et al – J Clin Invest.

Animal mycobiome

The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet – Mims and Al Abdallah et al. – Communications Biology

Profound mycobiome differences between segregated mouse colonies do not influence Th17 responses to a newly introduced gut fungal commensal. – Doron et al. – Fungal Genet Biol.

Season, age, and sex affect the fecal mycobiota of free-ranging Tibetan macaques (Macaca thibetana). – Sun et al – Am J Primatol.

Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. – Yeung et al – Cell Host Microbe. 

Mycobiome techniques

The fungal frontier: a comparative analysis of methods used in the study of the human gut mycobiome. – Huseyin et al. – Front Microbiol. 

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Karen et al. – Microbiome

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing – Lind et al – Microbiome

Tiara: Deep learning-based classification system for eukaryotic sequences –  Karlicki et al – bioRxiv.org

~ Kent Willis, MD