August 28, 2021


Free Webinar: Convergence Of Circadian Rhythms And Gut Microbes: Maintaining The Metronome Of Life – September 7, 2021 (10:00 am – 11:00 am) – Organized by The Institute for the Advancement of Food and Nutrition Sciences


Review: The importance of Faecalibacterium prausnitzii in human health and diseases – M Parsaei – New Microbes and New Infections

Review: The gut microbiome in feast and famine – Hannah D Holscher – Nature Reviews Gastroenterology & Hepatology

Prophylactic Administration of a Bacteriophage Cocktail Is Safe and Effective in Reducing Salmonella enterica Serovar Typhimurium Burden in Vivo – Quentin Lamy-Besnier – Microbiology Spectrum

Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users – Divya Gopinath – Clinical Oral Investigations

Cross-sectional comparisons of subgingival microbiome and gingival fluid inflammatory cytokines in periodontally healthy vegetarians versus non-vegetarians – Ahmed Khocht – Journal of Periodontal Research

Human and General Microbiome

Review: Gut microbiota as the critical correlation of polycystic ovary syndrome and type 2 diabetes mellitus. – Liyun Duan – Biomedicine & Pharmacotherapy

Review: The Gut Microbiome, Metformin, and Aging – Sri Nitya Reddy Induri – Annual Review of Pharmacology and Toxicology

Review: Microbe defines the efficacy of chemotherapeutic drug: A complete paradigm – P Dalal – FEMS Microbiology Letters

Review: Gut Microbiota Profiles in Early- and Late-Onset Colorectal Cancer: A Potential Diagnostic Biomarker in the Future – Murdani Abdullah – Digestion

Review: Manipulating the neonatal gut microbiome: current understanding and future perspectives. – Emma Wong – Archives of Disease in Childhood

Review: Dietary advanced glycation end-products elicit toxicological effects by disrupting gut microbiome and immune homeostasis – Yingjia Chen – Journal of Immunotoxicology

Perspective: The microbiome extends host evolutionary potential – Lucas P Henry – Nature Communications

Perspective: How microbiota improve immunotherapy – Eduard Ansaldo – Science

Alterations in microbiota and their metabolites are associated with beneficial effects of bile acid sequestrant on icteric primary biliary Cholangitis – Bo Li – Gut Microbes

The gut microbiome in sickle cell disease: Characterization and potential implications – Hassan Brim – PloS ONE

Bacterial resistance to CRISPR-Cas antimicrobials – Ruben V Uribe – Scientific Reports

Depression: A Gut Microbiome Feeling! – Ahmed Naguy – The Journal of Nervous and Mental Disease

The potential prebiotic effect of 2-Butyloctanol on the human axillary microbiome – Min Li – International Journal of Cosmetic Science

Fecal Bacteria as Non-Invasive Biomarkers for Colorectal Adenocarcinoma – Biao Yuan – Frontiers in Oncology

Beneficial Compounds and Microbes

Review: Molecular genetics for probiotic engineering: dissecting lactic acid bacteria – Ronit Suissa – Trends in Microbiology

The effect of probiotic supplementation on the gut microbiota of preterm infants – Erica L Plummer – Journal of Medical Microbiology

Noni (Morinda citrifolia L.) Fruit Polysaccharides Regulated IBD Mice Via Targeting Gut Microbiota: Association of JNK/ERK/NF-κB Signaling Pathways – Ming-Yu Jin – Journal of Agricultural and Food Chemistry

Long-term personalized low FODMAP diet improves symptoms and maintains luminal Bifidobacteria abundance in irritable bowel syndrome – Heidi M Staudacher – Neurogastroenterology and Motility

New Lactiplantibacillus plantarum and Lacticaseibacillus rhamnosus strains: well tolerated and improve infant microbiota – Gunilla Önning – Pediatric Research

Multi-targeted properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 against enterotoxigenic Escherichia coli (ETEC) H10407 pathogenesis across human gut models – Charlène Roussel – Gut Microbes

Animal Microbiome 

Review: A role for bacterial experimental evolution in coral bleaching mitigation? – Justin Maire – Trends in Microbiology

Microbial bioindicators of Stony Coral Tissue Loss Disease identified in corals and overlying waters using a rapid field-based sequencing approach – Cynthia C Becker – Environmental Microbiology

Assessing age, breeding stage, and mating activity as drivers of variation in the reproductive microbiome of female tree swallows – Jessica Hernandez – Ecology and Evolution

Study in Drosophila: Activation of innate immunity during development induces unresolved dysbiotic inflammatory gut and shortens lifespan – Kyoko Yamashita – Disease Models & Mechanisms

Study in Mice: The composition of the gut microbiota following early-life antibiotic exposure affects host health and longevity in later life – Miriam A Lynn – Cell Reports

Study in Mice: Redundant cytokine requirement for intestinal microbiota-induced Th17 cell differentiation in draining lymph nodes – Teruyuki Sano – Cell reports

Honeybee intestines retain low yeast titers, but no bacterial mutualists, at emergence. – James P Tauber – Yeast (Wiley)

The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans – Jaelle C Brealey – Current Biology

Breed differences in the expression levels of gga-miR-222a in laying hens influenced H(2)S production by regulating methionine synthase genes in gut bacteria – Si-Cheng Xing – Microbiome

Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the  Southeastern United States – Jesse C Thomas IV – Microbiology spectrum

Ingestion of Lactobacillus rhamnosus modulates chronic stress-induced feather pecking in chickens – Claire Mindus – Scientific Reports

Wolves, dogs and humans in regular contact can mutually impact each other’s skin microbiota. – Stefanie Urimare Wetzels – Scientific Reports

Label-free proteomic analysis reveals differentially expressed Wolbachia proteins in Tyrophagus putrescentiae: Mite allergens and markers reflecting population-related  proteome differences – Tomas Erban – Journal of Proteomics

Teaching old mice new tricks: the utility of aged mouse models of C. difficile infection to study pathogenesis and rejuvenate immune response – Jae Hyun Shin – Gut Microbes

Soil and Plant Microbiome

Review: A review of root exudates and rhizosphere microbiome for crop production – Haishu Sun – Environmental Science and Pollution Research International

The biodiversity effect of reduced tillage on soil microbiota – Tobias Guldberg Frøslev – Ambio

Microbiome-mediated response to pulse fire disturbance outweighs the effects of fire legacy on plant performance – Daniel Revillini – The New Phytologist

Interactions between soil compositions and the wheat root microbiome under drought stress: From an in silico to in planta perspective – Jiyeon Si – Computational and Structural Biotechnology Journal

Environmental Science

Review: Temporal and Spatial Signaling Mediating the Balance of the Plankton Microbiome – Yun Deng – Annual Review of Marine Science

Protocols, Methods and Techniques

Archive for Research in Child Health (ARCH) and Baby Gut: Study Protocol for a Remote, Prospective, Longitudinal Pregnancy and Birth Cohort to Address Microbiota  Development and Child Health – Eliot N Haddad – Methods and Protocols

Benchmarking laboratory processes to characterise low-biomass respiratory microbiota – Raiza Hasrat – Scientific Reports

Simultaneous feature selection and outlier detection with optimality guarantees – Luca Insolia – Biometrics

SMDI: An Index for Measuring Subgingival Microbial Dysbiosis – T Chen – Journal of dental researchTrends in inflammatory bowel disease treatment in the past two decades-a high-level text mining analysis of PubMed publications – Eyal Klang – United European Gastroenterology Journal

August 15, 2021

Have a nice Sunday! Today in this Digest, we want to highlight a study that found the effect of human gastric microbiota on premalignant lesions in mice; additionally, new studies about microbiome and Alzheimer’s, relationships between Oxalobacter formigenes and oxalate excretion. Also, we highlight two studies about the role of the coral microbiome and the metapangenome of the significantly ubiquitous SAR324 lineage.   


Human Gastric Microbiota Transplantation Recapitulates Premalignant Lesions In germ-free mice – Soon-Kyeong Kwon – Gut

Effect Of Antibiotic Treatment On Oxalobacter formigenes Colonization Of The Gut microbiome and urinary oxalate excretion – Lama Nazzal – Scientific Reports

Disturbed Microbial Ecology In Alzheimer’s Disease: Evidence From The Gut Microbiota and fecal metabolome – Jianxiong Xi – BMC Microbiology

The Impact Of Enriched Resistant Starch Type-2 Cookies On The Gut Microbiome In Hemodialysis Patients: A Randomized Controlled Trial – Julie Ann Kemp – Molecular Nutrition & Food Research

Coral Microbiome Manipulation Elicits Metabolic And Genetic Restructuring To Mitigate Heat Stress And Evade Mortality – Erika P Santoro – Science Advances

Metapangenomics Reveals Depth-dependent Shifts In Metabolic Potential For The ubiquitous marine bacterial SAR324 lineage – Dominique Boeuf – Microbiome

A. muciniphila Suppresses Colorectal Tumorigenesis By Inducing TLR2/NLRP3-Mediated M1-Like TAMs – Lina Fan – Cancer Immunology Research

Human and General Microbiome

Review: Genes, Environment, And Developmental Timing: New Insights From Translational Approaches To Understand Early Origins Of Respiratory Diseases – Maria J Gutierrez – Pediatric Pulmonology

Review: Contribution Of Biotransformations Carried Out By The Microbiota, Drug-metabolizing Enzymes, And Transport Proteins To The Biological Activities Of Phytochemicals Found In The Diet – Anna Boronat – Advances In Nutrition

Review: The Power And Potential Of Biomap To Elucidate Host-microbiome Interplay In Skin Inflammatory Diseases – Harri Alenius – Experimental Dermatology

Review: Colliding And Interacting Microbiomes And Microbial Communities And Consequences For Human Health – Susan Mills – Environmental Microbiology

Review: Tralokinumab In Atopic Dermatitis – Andreas Wollenberg –Journal Of The German Society of Dermatology 

Review: Skin Microbiome-The Next Frontier For Probiotic Intervention – Isabella J McLoughlin – Probiotics And Antimicrobial Proteins

Minireview: Pathogenic Mechanisms Of Trimethylamine N-oxide-induced Atherosclerosis And Cardiomyopathy – Youjing Zheng – Current Vascular Pharmacology

Gut Microbiome Diversity And Composition Are Associated With Habitual Dairy Intakes: A Cross-sectional Study In Men – Hajara Aslam – The Journal Of Nutrition

Gut Microbiota Profiles And The Role Of Anti-CdtB And Anti-vinculin Antibodies In Patients with FGID – Riccardo Vasapolli – European Journal Of Clinical Investigation

Small Intestinal Bacterial Overgrowth In Patients With Inflammatory Bowel Disease: A case-control study – Uday C Ghoshal – Indian Journal Of Gastroenterology

Position paper: Dangerous Liaisons: Bacteria, Antimicrobial Therapies And Allergic Diseases – Gerdien Tramper-Stranders – Allergy

PD-L1(+) And XCR1(+) Dendritic Cells Are Region-specific Regulators Of Gut Homeostasis – Thais G Moreira – Nature Communications

Simulated Digestion And Fecal Fermentation Behaviors Of Exopolysaccharides From Paecilomyces cicadae Tjj1213 And Its Effects On Human Gut Microbiota – Juanjuan Tian – International Journal Of Biological Macromolecules

Beneficial Microbes, Compounds, and Interventions

Gut Microbiome-short-chain Fatty Acids Interplay In The Context Of Iron Deficiency anaemia – Ana Soriano-Lerma – European Journal Of Nutrition

Chicory Inulin Enhances Fermentation Of 2′-fucosyllactose By Infant Fecal Microbiota and differentially influences immature dendritic cell and T-cell cytokine responses  under normal and Th2-polarizing condition – Renate Akkerman – Food & Function

The Gut Microbiota Mediates The Protective Effects Of Anserine Supplementation On hyperuricaemia and associated renal inflammation. – Jiaojiao Han – Food & Function

Review: Monoterpenes: Current Knowledge On Food Source, Metabolism, And Health Effects – José Fernando Rinaldi de Alvarenga – Critical Reviews In Food Science And Nutrition

Review: Mushrooms On The Plate: Trends Towards NAFLD Treatment, Health Improvement And sustainable diets – Adriana Fontes – European Journal Of Clinical Investigation

Review: Low-Dose Lactulose As A Prebiotic For Improved Gut Health And Enhanced Mineral Absorption. – Tarkan Karakan – Frontiers In Nutrition

Animal Microbiome

Probiotic Lactobacilli Administration Induces Changes In The Fecal Microbiota Of Preweaned Dairy Calves – Sofía Fernández-Ciganda – Probiotics And Antimicrobial Proteins

Metformin Alleviates Choline Diet-induced TMAO Elevation In C57BL/6J Mice By influencing gut-microbiota composition and functionality – Chunyan Su – Nutrition & Diabetes

Phylosymbiotic Structures Of The Microbiota In Mollitrichosiphum Tenuicorpus (Hemiptera: Aphididae: Greenideinae). – Man Qin – Microbial Ecology

Impaired Skeletal Muscle Hypertrophy Signaling And Amino Acid Deprivation Response In ApoE Knockout Mice With An Unhealthy Lipoprotein Distribution – Jakob Agergaard – Scientific Reports

Effect Of Black Ginseng And Silkworm Supplementation On Obesity, The Transcriptome, and the gut microbiome of diet-induced overweight dogs – Miey Park – Scientific Reports

Juvenile Social Defeat Stress Exposure Favors In Later Onset Of Irritable Bowel syndrome-like symptoms in male mice – Kenjiro Matsumoto – Scientific Reports

Plant Microbiome

Plant Developmental Stage Drives The Differentiation In Ecological Role Of The Maize microbiome. – Chao Xiong – Microbiome

Impact Of Biocontrol Microbes On Soil Microbial Diversity In Ginger (Zingiber officinale Roscoe). – Zhiqiang Huang – Pest Management Science

Environmental Microbiome

16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes In Deep-Sea Benthic Foraminifera – Iines S Salonen – Frontiers In Microbiology

Microbial Community Composition Controls Carbon Flux Across Litter Types In Early Phase Of Litter Decomposition – Marie E Kroeger – Environmental Microbiology

Contribution Of Stochastic Processes To The Microbial Community Assembly On Field-collected Microplastics – Yuanze Sun – Environmental Microbiology


Review: Simultaneous Ribosome Profiling Of Hundreds Of Microbes From The Human Microbiome – Brayon J Fremin – Nature Protocols

August 4, 2021

Have a nice day!! Today, in this Digest: a study of the microbiome structure and host relationship in a Korean population, Microbiome and vitamin D3, microbiome and cystic fibrosis, a study about Faecalibacterium prausnitzii diversity under liver cirrhosis, and more! 

Human and General Microbiome

Review: Clostridioides difficile Infection in Pediatric Inflammatory Bowel Disease: A Clinician’s Dilemma – Máire A Conrad – Journal of the Pediatric Infectious Diseases Society

Minireview: The Gut-Lung Axis in Cystic Fibrosis – Courtney E Price – Journal of Bacteriology

Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis – Yaowen Chen – mSystems

Gut Microbiome Structure and Association with Host Factors in a Korean Population – Mi Young Lim – mSystems

Pilot trial of vitamin D3 and calcifediol in healthy vitamin D deficient adults: does it change the fecal microbiome? – Albert Shieh – The Journal of Clinical Endocrinology and Metabolism

Deciphering the role of skin surface microbiome in skin health: an integrative multi-omics approach reveals three distinct metabolite-microbe clusters – Pierre-François Roux – The Journal of Investigative Dermatology

Preprint: Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation. – Mericien Venzon – Research Square

Novel microbiota-related gene set enrichment analysis identified osteoporosis associated gut microbiota from autoimmune diseases – Rong-Rong Cao – Journal of Bone and Mineral Metabolism

Sulfation of Arabinogalactan Proteins Confers Privileged Nutrient Status to Bacteroides plebeius – Jose Munoz-Munoz – mBio

Beneficial Microbes, Compounds, and Interventions

Review: Bifidobacterium longum: Protection against Inflammatory Bowel Disease – Shunyu Yao – Journal of Immunology Research

Gluten-free diet can ameliorate the symptoms of non-celiac autoimmune diseases – Aaron Lerner – Nutrition Reviews

Protein supplementation during an energy-restricted diet induces visceral fat loss and gut microbiota amino acid metabolism activation: a randomized trial – Pierre Bel Lassen – Scientific Reports

Food Microbiome

Metabolic Features of Ganjang (a Korean Traditional Soy Sauce) Fermentation Revealed by Genome-Centered Metatranscriptomics – Byung Hee Chun – mSystems

Animal Microbiome

Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome. – Sahana Kuthyar – mSystems

Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance – Christian R Voolstra – Molecular Ecology

Plant Microbiome

Site and Organ-Specific Culture-Dependent Endophytic Diversity of Crocus sativus L (Saffron) in Kashmir Himalaya, India. – Bushra Jan – Microbial ecology

Microbiome and Environment

Biodegradation of metoprolol in oxic and anoxic hyporheic zone sediments: unexpected effects on microbial communities – Cyrus Rutere – Applied Microbiology and Biotechnology

Microbial assemblages and methanogenesis pathways impact methane production and foaming in manure deep-pit storages – Fan Yang – PloS One

Preprint: Multi-plasmid clash in a bacterial community: plasmid viability depends on the ecological setting of hosts – Cindy Given – bioRxiv

Preprint: Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling – Panagiotis S. Adam – bioRxiv

Microbiome and Forensic Research

Touch microbiome as a potential tool for forensic investigation: A pilot study – Noemi Procopio – Journal of Forensic and Legal Medicine

July 27, 2021

Have a nice day! Before presenting the Digest for today, I want to highlight that in few hours the ISME-LatinAmerica 2021 meeting will start. Additionally, I also want to highlight a Call from the Institut Pasteur for the creation of new groups (applications available until next November 30). Now, enjoy this digest!

Human and General Microbiome

Review: Discovery and mining of enzymes from the human gut microbiome – Baolei Jia – Trends in Biotechnology

Review: Antimicrobial peptides and proteins: Interaction with the skin microbiota – Franziska Rademacher – Experimental Dermatology

Review: Malnutrition and the microbiome as modifiers of early neurodevelopment – Elena J L Coley – Trends in Neurosciences

Review: Predictors of multidrug resistant Pseudomonas aeruginosa involvement in bloodstream infections – Sabina Herrera – Current Opinion in Infectious Diseases

Review: Diet Interventions for Irritable Bowel Syndrome: Separating the Wheat from the Chafe. – Emily Haller – Gastroenterology Clinics of North America

Review: Emerging Role of the Gut Microbiome in Irritable Bowel Syndrome – Prashant Singh – Gastroenterology Clinics of North America

Review: The Types and Proportions of Commensal Microbiota Have a Predictive Value in Coronary Heart Disease. – Lin Chen – Journal of Clinical Medicine

Review: Association of Microbiome with Oral Squamous Cell Carcinoma: A Systematic Review of the Metagenomic Studies. – Lee Su Mun – International Journal of Environmental Research and Public Health

Book Chapter: The Role of H(2)S in the Gastrointestinal Tract and Microbiota – Ailin Xiao – Advances in Hydrogen Sulfide Biology 

Research Highlight: CNMa-CNMa receptor at microbiome-gut-brain axis: novel target to regulate feeding decision – Liyuan Peng – Signal Transduction and Targeted Therapy

Household environmental microbiota influences early-life eczema development – Le Duc Huy Ta – Environmental Microbiology

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment – Morteza Roodgar – Genome Research

Combined mechanical and oral antibiotic bowel preparation is associated with prolonged recurrence-free survival following surgery for colorectal cancer – Lindsey M Zhang – Journal of Surgical Oncology

Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections. – Katharina Stracke – PLoS Neglected Tropical Diseases

Characteristics of the bacterial microbiota in the upper respiratory tract of children – Wei Cao – European archives of Oto-rhino-laryngology

Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing – Yuanfeng Liu – Frontiers in Molecular Biosciences

The Intestinal Microbiome Predicts Weight Loss on a Calorie-Restricted Diet and Is Associated With Improved Hepatic Steatosis – Tien S Dong – Frontiers in Nutrition

16S rRNA gene amplicon sequencing of gut microbiota in gestational diabetes mellitus and their correlation with disease risk factors – J Wei – Journal of Endocrinological Investigation

Analyses of publicly available Hungatella hathewayi genomes revealed genetic distances indicating they belong to more than one species – Laura E Hernández-Juárez – Virulence

Estrogen-related receptor alpha (ERRα) is a key regulator of intestinal homeostasis and protects against colitis – Allan Tran – Scientific Reports

Predicting dental caries increment using salivary biomarkers in a remote Indigenous Australian child population – Surani Fernando – BMC Oral Health

Beneficial Microbes, Treatments, and Compounds

Human milk oligosaccharide 2′-fucosyllactose supplementation improves gut barrier function and signaling in the vagal afferent pathway in mice – Sunhye Lee – Food & Function

Lactobacillus casei LC89 exerts antidiabetic effects through regulating hepatic glucagon response and gut microbiota in type 2 diabetic mice – Yongli Zhang – Food & Function

The roles of different Bacteroides fragilis strains in protecting against DSS-induced ulcerative colitis and related functional genes – Chen Wang – Food & Function

Probiotics Fermentation Technology, a Novel Kefir Product, Ameliorates Cognitive Impairment in Streptozotocin-Induced Sporadic Alzheimer’s Disease in Mice – Nesrine S El Sayed – Oxidative Medicine and Cellular Longevity

Vaccarin enhances intestinal barrier function in type 2 diabetic mice – Jiang-Nan Sun – European Journal of Pharmacology

Personalized Postprandial Glucose Response-Targeting Diet Versus Mediterranean Diet for Glycemic Control in Prediabetes – Orly Ben-Yacov – Diabetes Care

Animal Microbiome

Dietary supplementation of alpha-lipoic acid mitigates the negative effects of heat stress in broilers – Sanjeev Wasti – PloS One

On the move: sloths and their epibionts as model mobile ecosystems – Maya Kaup – Biological reviews of the Cambridge Philosophical Society

Plant Microbiome

The discovery of pivotal fungus and major determinant factor shaping soil microbial community composition associated with rot root of American ginseng. – Lixia Tian – Plant Signaling & Behavior

Environmental Microbiome

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction. – Najoua Mghazli – Frontiers in Microbiology

Characterization of eukaryotic microbiome and associated bacteria communities in a drinking water treatment plant – Patricia Soler – The Science of the Total Environment

Dynamics of bacterial and archaeal communities along the composting of tannery sludge – Ademir Sergio Ferreira Araujo – Environmental Science and Pollution Research International

Other Microbes

Prioritization of potential drug targets and antigenic vaccine candidates against Klebsiella aerogenes using the computational subtractive proteome-driven approach. – Vijina Chakkyarath – Journal of proteins and proteomics

Genomic evolution of antimicrobial resistance in Escherichia coli – Pimlapas Leekitcharoenphon – Scientific Reports

Microbiome Analysis Tools and Techniques

Strainberry: automated strain separation in low-complexity metagenomes using long reads. – Riccardo Vicedomini – Nature Communications

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging – Katharine M Ng – Journal of Visualized Experiments (JoVE)

A newly developed PCR-based method revealed distinct Fusobacterium nucleatum subspecies infection patterns in colorectal cancer – Dexi Bi – Microbial Biotechnology

A protocol for characterization of extremely preterm infant gut microbiota in double-blind clinical trials – Magalí Martí – STAR Protocols

Transformation and differential abundance analysis of microbiome data incorporating phylogeny – Chao Zhou – Bioinformatics

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)

July 09, 2021

Have a nice Friday! Today in this Digest, we highlight a study showing that two patients who received fecal transplants could resolve COVID19. We also highlight another study revealing differences between the microbiota from Tibetan and Han immigrants living at an altitude of 3,900 m. Today, this Digest also papers on many other topics.

Human and General Microbiome

Rapid Resolution Of COVID-19 After Faecal Microbiota Transplantation – Jarosław Biliński – Gut

Correlations Between Intestinal Microbial Community And Hematological Profile In Native Tibetans and Han Immigrants. – Yan Ma – Frontiers In Microbiology

Host-emitted Amino Acid Cues Regulate Bacterial Chemokinesis To Enhance colonization. – Catherine D Robinson – Cell Host & Microbe

Fecal Microbiota Transplant As A Potential Treatment For Parkinson’s Disease – A case series. – Arik Segal – Clinical Neurology And Neurosurgery

Translocated Microbiome Composition Determines Immunological Outcome In Treated HIV infection. – Krystelle Nganou-Makamdop – Cell

In-vivo Impact Of Common Cosmetic Preservative Systems In Full Formulation On The skin microbiome. – Barry Murphy – PloS One

Antibiotics Modulate Neoadjuvant Therapy Efficiency In Patients With Breast Cancer: a pilot analysis. – Xi Zhang – Scientific Reports

Fecal Sample Collection Methods And Time Of Day Impact Microbiome Composition And short chain fatty acid concentrations. – Jacquelyn Jones – Scientific Reports

The Association Between Serum Microbial DNA Composition And Symptoms Of Depression and anxiety in mood disorders. – Sang Jin Rhee – Scientific Reports

Gut Microbiota Signature Of Pathogen-dependent Dysbiosis In Viral Gastroenteritis – Taketoshi Mizutani – Scientific Reports

Translocation Of Vaginal Microbiota Is Involved In Impairment And Protection Of uterine health. – Jinfeng Wang – Nature Communications

Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model – Mary E Salliss – NPJ Biofilms And Microbiomes

Metagenome-wide Association Study Of Gut Microbiome Revealed Potential Microbial marker set for diagnosis of pediatric myasthenia gravis. – Peng Liu – BMC Medicine

Review: Theranostic Cells: Emerging Clinical Applications Of Synthetic Biology – Monica P McNerney – Nature Reviews Genetics

Review: Current And Future Biomarkers In Alcoholic Hepatitis – Stephanie M Rutledge – Clinics In Liver Disease

Review: Role Of Bile Acids In Inflammatory Liver Diseases – Ioannis Evangelakos – Seminars In Immunopathology

Microbiome, Food and Diet

Review: Interference Of Dietary Polyphenols With Potentially Toxic Amino Acid Metabolites derived from the colonic microbiota – Naschla Gasaly – Amino Acids

Suppressed Inflammation In Obese Children Induced By A High-fiber Diet Is Associated with the attenuation of gut microbial virulence factor genes. – Hui Li – Virulence

Technological And Environmental Features Determine The Uniqueness Of The Lambic Beer Microbiota And Production Process – Dries Bongaerts – Applied And Environmental Microbiology

Role Of Dietary Fiber In Safeguarding Intestinal Health After Pelvic Radiotherapy – Cecilia Bull – Current Opinion In Supportive And Palliative Care

Animal Microbiome

Captivity Reduces Diversity And Shifts Composition Of The Brown Kiwi Microbiome – Priscilla A San Juan – Animal Microbiome

Plant Microbiome

Nitrogen Deficiency-induced Bacterial Community Shifts In Soybean Roots – Wataru Yazaki – Microbes And Environments

Review: Metabolic Interactions In Beneficial Microbe Recruitment By Plants – Davar Abedini – Current Opinion In Biotechnology

Beneficial Microbes and Compounds

Matrix Effects On The Delivery Efficacy Of Bifidobacterium animalis subsp. lactis BB-12 on Fecal Microbiota, Gut Transit Time, and Short-Chain Fatty Acids in Healthy Young Adults – Zhaoyong Ba – mSphere

Exopolysaccharides From Lactobacillus plantarum NCU116 Facilitate Intestinal Homeostasis by Modulating Intestinal Epithelial Regeneration and Microbiota. – Xingtao Zhou – Journal Of Agricultural And Food Chemistry

Effect Of Herbal Medicine Daikenchuto On Gastrointestinal Symptoms Following laparoscopic colectomy in patients with colon cancer: A prospective randomized study. – Keita Hanada – Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie

Effects of co-fermented collagen peptide-jackfruit juice on the immune response and gut microbiota in immunosuppressed mice. – Tingting Ma – Food Chemistry

Review: Bacteriophage-mediated Modulation Of Microbiota For Diseases Treatment – Yu Zhang – Advanced Drug Delivery Reviews


Whole-Genome Sequencing Of Mycobacterium tuberculosis Directly From Sputum Samples – Amanda Claire Brown – Methods In Molecular Biology 

RecT Recombinase Expression Enables Efficient Gene Editing In Enterococcus – Victor Chen – Applied And Environmental Microbiology

July 4, 2021

Have a nice Sunday! (and a happy July 4th to Americans!) In this digest, we have a set of papers covering different areas of microbiome research, including 3 studies covering aspects of the relationship between COVID19 and microbiome, pan-genomic, and metatranscriptomic studies from probiotic microbes, and the role of the aryl hydrocarbon receptor in the host-microbiome communication.   

Human and General Microbiome

Review: The Relationship Between The Gut Microbiome And Neurodegenerative Diseases – Xueling Zhu – Neuroscience Bulletin

Systematic Review: Exploring The Role Of Respiratory Microbiome In Lung Cancer: A Systematic Review – Fabiana Perrone – Critical Reviews In Oncology/Hematology

Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling through the aryl hydrocarbon receptor – Aayushi Uberoi – Cell Host & Microbe

Tryptophan-metabolizing Gut Microbes Regulate Adult Neurogenesis Via The Aryl hydrocarbon receptor – George Zhang Wei – Proceedings Of The National Academy Of Sciences Of The United States Of America

Mucosa-associated Gut Microbiota Reflects Clinical Course Of Ulcerative Colitis – Yuichiro Nishihara – Scientific Reports

Helicobacter pylori Infection-induced Changes In The Intestinal Microbiota Of 14-year-old or 15-year-old Japanese adolescents: a cross-sectional study – Toshihiko Kakiuchi – BMJ Open

The Infant Gut Resistome Is Associated With E. coli And Early-life Exposures – Rebecca M Lebeaux – BMC Microbiology

The Gut Microbiome Of Heart Failure With Preserved Ejection Fraction – Anna L Beale – Journal Of The American Heart Association

Association Of Gut Microbiomes With Lung And Esophageal Cancer: A Pilot Study – Weitao Shen – World Journal Of Microbiology & Biotechnology

Vaginal Lactobacilli And Vaginal Dysbiosis-Associated Bacteria Differently Affect Cervical Epithelial and Immune Homeostasis and Anti-Viral Defenses – Sabrina Nicolò – International Journal Of Molecular Sciences

Finding A Balance In The Vaginal Microbiome: How Do We Treat And Prevent The Occurrence of Bacterial Vaginosis? – Rebecca Jane Joseph – Antibiotics (MDPI)

Mycobiome And Cancer: What Is The Evidence? – Natalia Vallianou – Cancers

Characterizing The Effects Of Calcium And Prebiotic Fiber On Human Gut Microbiota Composition and Function Using a Randomized Crossover Design-A Feasibility Study – Lara S Yoon – Nutrients

Gut Microbiota Profile And Its Association With Clinical Variables And Dietary Intake in Overweight/Obese and Lean Subjects: A Cross-Sectional Study – Judit Companys – Nutrients

Microbiome and COVID19

Review: Modulation Of Gut Microbiota For The Prevention And Treatment Of COVID-19 – Jiezhong Chen – Journal Of Clinical Medicine

COVID-19 Lockdowns May Reduce Resistance Genes Diversity In The Human Microbiome And the Need for Antibiotics – João S Rebelo – International Journal Of Molecular Sciences

Reversion Of Gut Microbiota During The Recovery Phase In Patients With Asymptomatic or Mild COVID-19: Longitudinal Study  – Han-Na Kim – Microorganisms

Beneficial Microbes and Compounds

Flavonoids From Whole-Grain Oat Alleviated High-Fat Diet-Induced Hyperlipidemia Via Regulating Bile Acid Metabolism and Gut Microbiota in Mice – Ruiqian Duan – Journal Of Agricultural And Food Chemistry

Novel Targeted Biological Agents For The Treatment Of Atopic Dermatitis – Nan Yang – BioDrugs 

Escherichia coli Nissle 1917 As Adjuvant Therapy In Patients With Chronic Bacterial prostatitis: a non-blinded, randomized, controlled trial – Celeste Manfredi – World Journal Of Urology

Influence Of Lactobacillus Paracasei HII01 Supplementation On Glycemia And Inflammatory Biomarkers in Type 2 Diabetes: A Randomized Clinical Trial – Parichart Toejing – Foods (MDPI) 

Dietary Habits And Gut Microbiota In Healthy Adults: Focusing On The Right Diet. A Systematic Review – Giulia Gibiino – International Journal Of Molecular Sciences

Animal Microbiome

Review: Potential Of Bacillus velezensis As A Probiotic In Animal Feed: A Review – Fatima Khalid – Journal Of Microbiology

Metagenomics Analysis Revealed The Distinctive Ruminal Microbiome And Resistive profiles in dairy buffaloes – Hui-Zeng Sun – Animal Microbiome

Composition And Diversity Of Gut Microbiota In Pomacea canaliculata In Sexes And between developmental stages – Lian Chen – BMC Microbiology

Plant and Soil Microbiome

Microbiome-mediated Effects Of Habitat Fragmentation On Native Plant Performance – Kasey N Kiesewetter – The New Phytologist

Improvement Of Soil Microbial Diversity Through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food  Quality and Human Safety – Marta Bertola – Microorganisms (MDPI)

Leaf Metabolic Influence Of Glyphosate And Nanotubes On The Arabidopsis Thaliana phyllosphere – Mingjing Ke – Journal Of Environmental Sciences

Bioinformatics and Genomics

Comprehensive Pan-Genome Analysis Of Lactiplantibacillus plantarum Complete Genomes– Francesco M Carpi – Journal Of Applied Microbiology

Metagenomic And Metatranscriptomic Profiling Of Lactobacillus casei Zhang In The Human Gut – Jicheng Wang – NPJ Biofilms And Microbiomes

PhyLoSTM: A Novel Deep Learning Model On Disease Prediction From Longitudinal microbiome data – Divya Sharma – Bioinformatics

Joint Modeling Of Zero-inflated Longitudinal Proportions And Time-to-event Data With application to a gut microbiome study. – Jiyuan Hu – Biometrics

Microbiome and COVID19: some research highlights

Page created on June 20, 2021

Last update: July 4, 2021

The following quote from the translated abstract of the article Management Of COVID-19: The Zhejiang Experience Kaijin Xu et al., from the Journal Of Zhejiang University, mentioned:

Some patients with COVID-19 showed intestinal microbial dysbiosis with decreased probiotics such as Lactobacillus and Bifidobacterium, so nutritional and gastrointestinal function should be assessed for all patients. Nutritional support and application of prebiotics or probiotics were suggested to regulate the balance of intestinal microbiota and reduce the risk of secondary infection due to bacterial translocation.

As far as we could found, this text is the first report (published in the first half of May 2020) mentioning the influence of COVID19 on the gut microbiome composition. More information has been published in recent months about the links between this pandemic and the microbiome. This search included not only the respiratory microbiome but also those communities from the gut. 

In this post, we present a list of remarkable papers covering connections between microbiome and COVID19. If you have more suggestions, please tell us in the comments.

General and Respiratory Tract Microbiome

Metatranscriptomic Characterization Of COVID-19 Identified A Host Transcriptional Classifier Associated With Immune Signaling –  Haocheng Zhang – Clinical Infectious Diseases (published in May 2020)

The Lung Tissue Microbiota Features Of 20 Deceased Patients With COVID-19 – Jun Fan – The Journal Of Infection  (published in June 2020)

Nasopharyngeal Microbiota Profiling Of SARS-CoV-2 Infected Patients – Flavio De Maio- Biological Procedures Online (published in July 2020)

Metagenomic Next-Generation Sequencing Of Nasopharyngeal Specimens Collected From Confirmed and Suspect COVID-19 Patients – Heba H Mostafa – mBio  (published in November 2020)

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment – Jeremiah J. Minich – Microbiome (published in January 2021)

Variability In Digestive And Respiratory Tract Ace2 expression Is associated with the microbiome – Sean T Koester – PloS One (published in March 2021)

Functional Profiling Of COVID-19 Respiratory Tract Microbiomes – Niina Haiminen – Scientific Reports (published in March 2021)

Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19 – Maria Paz Ventero – Frontiers in Microbiology (Published in March, 2021)

Preprint: Signatures Of COVID-19 Severity And Immune Response In The Respiratory Tract microbiome – Carter Merenstein – MedRxiv (available from April 2021)

Preprint: Plasma Microbiome In COVID-19 Subjects: An Indicator Of Gut Barrier Defects And dysbiosis – Ram Prasad – BioRxiv (available from April 2021)

Evaluation Of Superinfection, Antimicrobial Usage, And Airway Microbiome With metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai – Qing Miao – Journal Of Microbiology, Immunology, And Infection (published in April 2021)

COVID-19 Influences Lung Microbiota Dynamics And Favors The Emergence Of Rare infectious diseases: A case report of Hafnia alvei pneumonia – Salvatore Lucio Cutuli – Journal Of Critical Care (published in April 2021)

The Lower Respiratory Tract Microbiome Of Critically Ill Patients With COVID-19 – Paolo Gaibani – Scientific Reports (available in May 2021)

Metagenomic Analysis Reveals Oropharyngeal Microbiota Alterations In Patients With COVID-19 –  Shengli Ma – Signal Transduction And Targeted Therapy (available in May 2021)

Preprint: Acute SARS-CoV-2 Infection Is Associated With An Expansion Of Bacteria Pathogens In the nose including Pseudomonas aeruginosa – Nicholas S Rhoades – BioRxiv (available from May 2021)

Nasopharyngeal Microbiota In SARS-CoV-2 Positive And Negative Patients – Phillip A Engen – Biological Procedures Online (published in June 2021)

SARS-CoV-2 Detection Status Associates With Bacterial Community Composition In patients and the hospital environment – Clarisse Marotz – Microbiome (published in June 2021)

Gut Microbiome studies

Gnotobiotic Rats Reveal That Gut Microbiota Regulates Colonic MRNA Of Ace2, The Receptor for SARS-CoV-2 Infectivity – Tao Yang- Hypertension (Published in May 2020)

Alterations In Gut Microbiota Of Patients With COVID-19 During Time Of Hospitalization – Tao Zuo – Gastroenterology (Published in May 2020)

Alterations In Fecal Fungal Microbiome Of Patients With COVID-19 During Time Of Hospitalization until Discharge – Tao Zuo – Gastroenterology (published in June 2020)

Maintaining standard volumes, efficacy and safety, of fecal microbiota transplantation for C. difficile infection during the COVID-19 pandemic: A prospective cohort study – Gianluca Ianiro – Digestive and Liver Diseases (Published in September 2020)

Gut Microbiota Composition Reflects Disease Severity And Dysfunctional Immune responses in patients with COVID-19 – Yun Kit Yeoh – Gut (published in January 2021)

The Faecal Metabolome In COVID-19 Patients Is Altered And Associated With Clinical features and gut microbes – Longxian Lv – Analytica Chimica Acta (published in January 2021)

The Intestinal And Oral Microbiomes Are Robust Predictors Of Covid-19 Severity The Main Predictor Of COVID-19-related Fatality – Doyle V. Ward – MedRxiv (available from Jan 2021)

16S rRNA Gene Sequencing Of Rectal Swab In Patients Affected By COVID-19 – Antonio Mazzarelli – PloS One (published in February 2021)

Investigation Of Nasal/Oropharyngeal Microbial Community Of COVID-19 Patients By 16S rDNA Sequencing – Martina Rueca – International Journal Of Environmental Research And Public Health (published in February 2021)

Integrated Gut Virome And Bacteriome Dynamics In COVID-19 Patients – Jiabao Cao – Gut Microbes  (published in March 2021)

Six-month Follow-up Of Gut Microbiota Richness In Patients With COVID-19 – Yanfei Chen – Gut (published in April 2021)

Gut Mycobiota Alterations In Patients With COVID-19 And H1N1 Infections And Their associations with clinical features – Longxian Lv – Communications Biology (published in April 2021)

Gut Microbiome And Resistome Changes During The First Wave Of The COVID-19 Pandemic in comparison with pre-pandemic travel-related changes – Ye Peng – Journal Of Travel Medicine (published in May 2021)

Gut microbiota, inflammation and molecular signatures of host response to infection – Wanglong Gou – Journal of Genetics and Genomics (published in May 2021)

Gut Microbiota May Not Be Fully Restored In Recovered COVID-19 Patients After 3-Month Recovery – Yu Tian – Frontiers In Nutrition (published in May 2021)

Gut Microbiome Composition Is Associated With COVID-19 Disease Severity – Pooja Patel – Gastroenterology  (published in May 2021)

The Gut Microbiome Of COVID-19 Recovered Patients Returns To Uninfected Status In A minority-dominated United States cohort – Rachel C Newsome – Gut Microbes (published in June 2021)

Reversion Of Gut Microbiota During The Recovery Phase In Patients With Asymptomatic or Mild COVID-19: Longitudinal Study  – Han-Na Kim – Microorganisms (published in June 2021)

Reviews, hypotheses, and other related topics

Divulgation post: Gut reaction: How the gut microbiome may influence the severity of COVID-19 – Shirin Moossavi and Marie-Claire Arrieta – The Conversation (June 21, 2020)

Intestinal Flora as a Potential Strategy to Fight SARS-CoV-2 Infection – Li-Hong He – Frontiers in Microbiology (Review; published in June 2020) 

Intestinal Permeability Changes With Bacterial Translocation As Key Events modulating systemic host immune response to SARS-CoV-2: A working hypothesis – Vincenzo Cardinale – Digestive And Liver Disease (published in September 2020)

The Potential Application Of Probiotics And Prebiotics For The Prevention And treatment of COVID-19 – Amin N Olaimat – NPJ Science Of Food (published in October 2020)

The Gut Microbiome: An Under-recognised Contributor To The COVID-19 Pandemic? – Jonathan P Segal – Therapeutic Advances In Gastroenterology  (published in November 2020)

Gut Microbiota in Covid-19: An unrecognised player? – Sabrina Donati Zeppa – Frontiers in Cellular and Infection Microbiology (Review, published in November 2020)

Is Gut Microbiota Dysbiosis A Predictor Of Increased Susceptibility To Poor Outcome of COVID-19 Patients? An Update – Carolina Ferreira – Microorganisms (published in December 2020)

Fecal microbiota transplantation for COVID-19; a potential emerging treatment strategy – Seyed Aria Nejadghaderi – Medical Hypotheses (Published in December 2020)

Do An Altered Gut Microbiota And An Associated Leaky Gut Affect COVID-19 Severity? – Heenam Stanley Kim – mBio (published in January 2021)

The Microbiome Of Bat Guano: For What Is This Knowledge Important? – Ivica Dimkić – Applied Microbiology And Biotechnology (published in January 2021)

Divulgation post: A healthy microbiome builds a strong immune system that could help defeat COVID-19 -Ana Maldonado-Contreras – The Conversation (January 22, 2021)

Microbiota Modulation Of The Gut-Lung Axis In COVID-19 – Gislane Lelis Vilela de Oliveira – Frontiers In Immunology (published in February 2021)

Next-Generation Sequencing Reveals The Progression Of COVID-19 – Xiaomin Chen – Frontiers In Cellular And Infection Microbiology (published in March 2021)

Metagenomics Approaches To Investigate The Gut Microbiome Of COVID-19 Patients – Sofia Sehli – Bioinformatics And Biology Insights (published in March 2021)

The Unique Impact of COVID-19 on Human Gut Microbiome Research – Ella Burchill – Frontiers in Medicine (Published in March 2021)

Review: Modulation Of Gut Microbiota For The Prevention And Treatment Of COVID-19 – Jiezhong Chen – Journal Of Clinical Medicine (Published in June 2021)


The author wants to thank Mauricio Morales (Undergraduate student; Universidad Mayor, Chile) for his help in the generation of this list.

Update (July 4, 2021). Thanks to MaximilianKohler and Rafael for their valuable suggestions for the list update.

June 19, 2021

Have a nice weekend (¡Tengan un muy buen fin de semana!) In this Digest, a set of papers released during this latter month were selected, covering some of the most remarkable articles for this week. Please, if you want to highlight another article, please suggest it in the comments.  


NGLess tutorial for processing metagenomes – Big Data Biology LabJune 25
Registration available (closing June 22) at:

Human and General Microbiome

The Bacterial Microbiota Of Hunner Lesion Interstitial Cystitis/Bladder Pain Syndrome – J Curtis Nickel – BJU International

Microbiome-encoded Bile Acid Metabolism Modulates Colonic Transit Times – Naisi Li – IScience

Psychobiotics For Patients With Chronic Gastrointestinal Disorders Having Anxiety Or Depression Symptoms – Viet Hang Dao – Journal Of Multidisciplinary Healthcare

Homeostasis Of Mucosal Glial Cells In Human Gut Is Independent Of Microbiota – Timna Inlender – Scientific Reports

Yearly Changes In The Composition Of Gut Microbiota In The Elderly, And The Effect of lactobacilli intake on these changes – Ryuta Amamoto – Scientific Reports

Don’t Worry, Heavy Moms; Just Eat Your Broccoli(or Kimchi)! Co-diet Of High-fiber and high-fat helps give birth to healthy offspring through gut microbiota-to-brain signaling –  Sun-Kyung Lee – Molecules And Cells

Dietary Fiber Intake, The Gut Microbiome, And Chronic Systemic Inflammation In A cohort of adult men – Wenjie Ma – Genome Medicine

Commentary: The Role Of The Microbiome In Inflammation During Tuberculosis – Anou M Somboro – EBioMedicine

Vaginal Bacterial Load In The Second Trimester Is Associated With Early Preterm birth recurrence: a nested case-control study – Laura Goodfellow – BJOG

Bacteria-Mediated Synergistic Cancer Therapy: Small Microbiome Has A Big Hope – Xinyu Lou – Nano-micro Letters

Spatial Heterogeneity Analysis Of The Human Virome With Taylor’s Power Law – Zhanshan Sam Ma – Computational And Structural Biotechnology Journal

The Influence Of Nutritional Factors On Immunological Outcomes – Evanthia Tourkochristou – Frontiers In Immunology

Gut Microbial SNPs Induced By High-Fiber Diet Dominate Nutrition Metabolism And Environmental Adaption of Faecalibacterium prausnitzii in Obese Children – Hui Li – Frontiers In Microbiology

Gut Microbiota Regulate Gut-Lung Axis Inflammatory Responses By Mediating ILC2 Compartmental Migration – Qinqin Pu – Journal Of Immunology

Effects Of Cat Ownership On The Gut Microbiota Of Owners – Guankui Du – PloS One

Effect Of COVID-19 Precautions On The Gut Microbiota And Nosocomial Infections – Armin Rashidi –  Gut Microbes

Association Between Oral Microflora And Gastrointestinal Tumors (Review)– Xiaoxiao Li – Oncology Reports

Bacteroides-dominant Gut Microbiome Of Late Infancy Is Associated With Enhanced neurodevelopment – Sukhpreet K Tamana – Gut Microbes

Proteome-wide Prediction Of Bacterial Carbohydrate-binding Proteins As A Tool For understanding commensal and pathogen colonisation of the vaginal microbiome – François Bonnardel  – NPJ Biofilms And Microbiomes

Investigating The Origin Of The Fetal Gut And Placenta Microbiome In Twins – Nayo Williams – The Journal Of Maternal-fetal & Neonatal Medicine

Levels Of Trimethylamine N-Oxide Remain Elevated Long Term After Left Ventricular Assist Device and Heart Transplantation and Are Independent From Measures of  Inflammation and Gut Dysbiosis – Melana Yuzefpolskaya – Circulation: Heart Failure

The Impact Of Device-assisted Therapies On The Gut Microbiome In Parkinson’s disease – Michal Lubomski – Journal Of Neurology

Alterations In Microbiome Composition And Metabolic Byproducts Drive Behavioral And transcriptional responses to morphine – Rebecca S Hofford – Neuropsychopharmacology

Structural Specificities Of Cell Surface Beta-glucan Polysaccharides Determine commensal yeast mediated immuno-modulatory activities – Changhon Lee – Nature Communications

Integrated Omics Endotyping Of Infants With Respiratory Syncytial Virus bronchiolitis and risk of childhood asthma – Yoshihiko Raita – Nature Communications

Fecal Short-chain Fatty Acids And Obesity In A Community-based Japanese Population: The DOSANCO Health Study – Ryodai Yamamura – Obesity Research & Clinical Practice

Anaerobic Microbiota Derived From The Upper Airways Impact Staphylococcus Aureus physiology –  Sarah K Lucas – Infection And Immunity

Review: A New Biological Triangle In Cancer: Intestinal Microbiota, Immune Checkpoint inhibitors and antibiotics – Jie Zhang – Clinical & Translational Oncology

The Microbiome And Gynecologic Cancer: Current Evidence And Future Opportunities – Laura M Chambers Current – Oncology Reports

Increased Bacterial Proteolytic Activity Detected Before Diagnosis Of Ulcerative Colitis – Heather J Galipeau – Inflammatory Bowel Diseases

Characterization Of An Alpha-glucosidase Enzyme Conserved In Gardnerella spp. Isolated from the human vaginal microbiome – Pashupati Bhandari – Journal Of Bacteriology

Catechin Metabolites Along With Curcumin Inhibit Proliferation And Induce Apoptosis in Cervical Cancer Cells by Regulating VEGF Expression In-Vitro – Elnaz Khojaste – Nutrition And Cancer

Review: The Lung Microbiome In Lung Transplantation – John E McGinniss – The Journal Of Heart And Lung Transplantation

Vaginal Microbiome: Normalcy Vs Dysbiosis – Viqar Sayeed Saraf – Archives Of Microbiology

Beneficial Microbes, Compounds and Interventions

Lactobacillus acidophilus LA14 Alleviates Liver Injury – Longxian Lv – mSystems

Desulfovibrio vulgaris, A Potent Acetic Acid-producing Bacterium, Attenuates nonalcoholic fatty liver disease in mice – Ying Hong – Gut Microbes

Review: The Interaction Of Akkermansia muciniphila With Host-derived Substances, Bacteria and diets – Tatsuro Hagi – Applied Microbiology And Biotechnology

Ganoderma lucidum Polysaccharide Modulates Gut Microbiota And Immune Cell Function to inhibit inflammation and tumorigenesis in colon – Cuiling Guo – Carbohydrate Polymers

The Outer Membrane Protein Amuc_1100 Of Akkermansia muciniphila Alleviates The depression-like behavior of depressed mice induced by chronic stress – Rongrong Cheng – Biochemical And Biophysical Research Communications

JianpiQinghua Granule Reduced PPI Dosage In Patients With Nonerosive Reflux Disease: A multicenter, randomized, double-blind, double-dummy, noninferiority study – Jiaqi Zhang –  Phytomedicine

Circadian Disruption-induced Metabolic Syndrome In Mice Is Ameliorated By Oat Beta-glucan mediated by gut microbiota – Wai-Yin Cheng – Carbohydrate Polymers

Effects Of Mediterranean Diet On Plasma Metabolites And Their Relationship With insulin resistance and gut microbiota composition in a crossover randomized clinical trial – Serena Galié – Clinical Nutrition

Calorie Restriction Conferred Improvement Effect On Long-term Rehabilitation Of ischemic stroke via gut microbiota Jia-Ting Huang – Pharmacological Research

Animal Models / Animal Microbiome

Holdemanella biformis Improves Glucose Tolerance And Regulates GLP-1 Signaling In obese mice –  Marina Romaní-Pérez – The FASEB Journal

Gut Microbiota Composition Affects Procyanidin A2-Attenuated Atherosclerosis In ApoE(-/-) Mice by Modulating the Bioavailability of Its Microbial Metabolites – Shiying Yang – Journal Of Agricultural And Food Chemistry

The Gut Microbiome Of The Sunda Pangolin (Manis javanica) Reveals Its Adaptation To specialized myrmecophagy – Fuhua Zhang – PeerJ

A Rise In Proteobacteria Is An Indicator Of Gut-liver Axis-mediated Nonalcoholic fatty liver disease in high-fructose-fed adult mice. Isabela Macedo Lopes Vasques-Monteiro – Nutrition Research

Plant Microbiome

Extension Of Plant Phenotypes By The Foliar Microbiome – Christine V Hawkes – Annual Review Of Plant Biology

Plant Genetics As A Tool For Manipulating Crop Microbiomes: Opportunities And Challenges – Kayla M Clouse – Frontiers In Bioengineering And Biotechnology

Development Of An Inexpensive Matrix-assisted Laser Desorption-time Of Flight Mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize – Michael G LaMontagne – PeerJ

Opinion: Assessing The Potential To Harness The Microbiome Through Plant Genetics – Joy Bergelson – Current Opinion In Biotechnology

Experimental and Computational Tools and Techniques

An Integrated Gene Catalog And Over 10,000 Metagenome-assembled Genomes From The gastrointestinal microbiome of ruminants – Fei Xie – Microbiome (BMC)

Antibiotic Resistance: Time Of Synthesis In A Post-genomic Age – Teresa Gil-Gil – Computational And Structural Biotechnology Journal

Efam: An Expanded, Metaproteome-supported HMM Profile Database Of Viral Protein families – Ahmed A Zayed – Bioinformatics

The Future Of Microbial Ecological Niche Theory And Modeling – Stephanie N Kivlin – The New Phytologist

DNA Extraction And Host Depletion Methods Significantly Impact And Potentially Bias Bacterial Detection in a Biological Fluid – Erika Ganda – mSystems


Electrical Conductivity As A Driver Of Biological And Geological Spatial heterogeneity in the Puquios, Salar de Llamara, Atacama Desert, Chile –  R P Reid – Scientific Reports