April 10, 2021

Have a nice weekend! Today, in this (late) Digest: articles about gut microbiome and COVID19 and neurological disorders, as well as other studies with skin, respiratory and vaginal microbiomes. We have also: wine microbiome, rumen eukaryotome, hydrocarbon degraders, some bioinformatic pipelines and more!

Human and General Microbiome

Faecalibacterium prausnitzii increases following fecal microbiota transplantation in recurrent Clostridioides difficile infection – Olle Björkqvist – PLoS ONE

Comprehensive profiling of the gut microbiota in patients with chronic obstructive pulmonary disease of varying severity – Yu-Chi Chiu –  PLoS ONE

Nutrition and the microbiota post-COVID-19 – G. G. F. Alberca – The Saudi Journal of Gastroenterology

Book Chapter: From “Leaky Gut” to Impaired Glia-Neuron Communication in Depression – Leszek Rudzki – Major Depressive Disorder

Skin microbiome of patients with interdigital tinea pedis: Corynebacterium striatum is more abundant in the patients – Mayumi Miyamoto – The Journal of Dermatology 

Selected Clostridia Strains from The Human Microbiota and their Metabolite, Butyrate, Improve Experimental Autoimmune Encephalomyelitis – Laura Calvo-Barreiro – Neurotherapeutics

Gut Microbiota Composition and Epigenetic Molecular Changes Connected to the Pathogenesis of Alzheimer’s Disease – Priyanka Nagu – Journal of Molecular Neuroscience 

Global climate change, diet, and the complex relationship between human host and microbiome: Towards an integrated picture – Francesco Catania – BioEssays

Global research trends in the microbiome related to irritable bowel syndrome: A bibliometric and visualized study – Sa’ed H Zyoud – World Journal of Gastroenterology

Coronavirus disease-2019 and the intestinal tract: An overview – Gabriela Gama Freire Alberca – World Journal of Gastroenterology

Comparison of Argentinean microbiota with other geographical populations reveals different taxonomic and functional signatures associated with obesity – Susana A. Pesoa – Scientific Reports 

Six-month follow-up of gut microbiota richness in patients with COVID-19 – Yanfei Chen – Gut (BMJ)

The combined therapy of fecal microbiota transplantation and laxatives for functional constipation in adults: A systematic review and meta-analysis of randomized controlled trials – Fang, Sijia MM – Medicine

Vaginal metabolic profiles during pregnancy: Changes between first and second trimester – Luca Laghi – PLoS ONE

Microbiome profiling of uncinate tissue and nasal polyps in patients with chronic rhinosinusitis using swab and tissue biopsy – Sung-Woo Cho – PLoS ONE

Patient attitudes towards faecal sampling for gut microbiome studies and clinical care reveal positive engagement and room for improvement – Laura A. Bolte – PLoS ONE

Microbes in the Media

Microbiome research in general and business newspapers: How many microbiome articles are published and which study designs make the news the most? – Andreu Prados-Bo – PLoS ONE

Food Microbiome

Minireview: The ecology of wine fermentation: a model for the study of complex microbial ecosystems – CG Conacher – Applied Microbiology and Biotechnology

Animal Microbiome

The rumen eukaryotome is a source of novel antimicrobial peptides with therapeutic potential – Lucy A. Onime – BMC Microbiology

The skin microbiota in equine pastern dermatitis: a case-control study of horses in Switzerland – Sarah Kaiser‐Thom – Veterinary Dermatology

Association between aging-dependent gut microbiome dysbiosis and dry eye severity in C57BL/6 male mouse model: a pilot study – Chang Ho Yoon – BMC Microbiology

Environmental Microbiome

Black Yeast Genomes Assembled from Plastic Fabric Metagenomes Reveal an Abundance of Hydrocarbon Degradation Genes – Osman Radwan – Microbiology Resource Annoucements

Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem – Claire E. Couch – PLoS ONE


A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota – Yafei Chang – Briefings in Bioinformatics

DisBalance: a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data – Fenglong Yang – Briefings in Bioinformatics

Review: Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms – Alla L. Lapidus – Frontiers in Microbiology

Built Environments

Analyzing indoor mycobiomes through a large-scale citizen science study in Norway – Sarah Kaiser‐Thom – Veterinary Dermatology

Forensic Microbiomes

Review: Microbiomes in forensic botany: a review – Sarah Ishak – Forensic Science, Medicine and Pathology 

Other papers

Untargeted Stable Isotope Probing of the Gut Microbiota Metabolome Using 13 C-Labeled Dietary Fibers – Pan Deng – Journal of Proteome Research

Metaproteomic sample preparation methods bias the recovery of host and microbial proteins according to taxa and cellular compartment – Patrick G.Gavin – Journal of Proteomics

April 3, 2021

Have a nice weekend! Today we want to highlight a new podcast about Microbiome and Health, available in Spotify. We also have today a set of studies, covering aspects of the urinary microbiome, drug-microbiome dynamics, and cancer microbiota.

Microbes in the Media

Biomes Podcast with Dr. Ruairi Robertson (Available in Spotify)

Human and General Microbiome

Microbiome and Metabolome Analyses Reveal Novel Interplay Between the Skin Microbiota and Plasma Metabolites in Psoriasis – Dongmei Chen – Frontiers in Microbiology

Microreview: Organ-on-chip to investigate host-pathogens interactions – Thomas Feaugas – Cellular Microbiology

Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol – Sara Dizzell – PLoS One

Urinary Microbiota; Which Non-Invasive Urine Collection Method Should We Use? – Muhammed Selcuk Ozer – IJCP

A specific association between laxative misuse and suicidal behaviours in patients with anorexia nervosa and bulimia nervosa – Aiste Lengvenyte – Eating and Weight Disorders – Studies on Anorexia, Bulimia and Obesity

Bile Microbiota in Liver Transplantation: Proof of Concept Using Gene Amplification in a Heterogeneous Clinical Scenario – Francesco D’Amico – Frontiers in Surgery

The Unique Impact of COVID-19 on Human Gut Microbiome Research – Ella Burchill – Frontiers in Medicine

Modeling of Urinary Microbiota Associated With Cystitis – Marina Ceprnja – Frontiers in Cellular and Infection Microbiology

Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema – Zhaoyan Chen – Frontiers in Cellular and Infection Microbiology

Analysis of Gut Microbiome Using Explainable Machine Learning Predicts Risk of Diarrhea Associated With Tyrosine Kinase Inhibitor Neratinib: A Pilot Study – Chi Wah Wong – Frontiers in Oncology 

Antitumor efficacy of a neoantigen cancer vaccine delivered by electroporation is influenced by microbiota composition – Lucia Lione – OncoImmunology 

Associations between dysbiosis-inducing drugs, overall survival and tumor response in patients treated with immune checkpoint inhibitors – Louis Gaucher – Therapeutic Advances in Medical Oncology

The Hygiene Hypothesis – Learning From but Not Living in the Past – Petra I. Pfefferle – Frontiers in Immunology

Strength Exercise Confers Protection in Central Nervous System Autoimmunity by Altering the Gut Microbiota – Hao Chen – Frontiers in Immunology

Beneficial Microbes and Compounds

Enrichment of Food With Tannin Extracts Promotes Healthy Changes in the Human Gut Microbiota – Silvia Molino – Frontiers in Microbiology

Bifidobacterium Lactis Probio-M8 regulates gut microbiota to alleviate Alzheimer’s disease in the APP/PS1 mouse model – Jianing Cao – European Journal of Nutrition 

Animal Microbiome

Re-Analysis of 16S rRNA Gene Sequence Data Sets Uncovers Disparate Laboratory-Specific Microbiomes Associated with the Yellow Fever Mosquito (Aedes aegypti) – Jonas Frankel-Bricker – Microbial Ecology 

FOXO regulates the expression of antimicrobial peptides and promotes phagocytosis of hemocytes in shrimp antibacterial immunity – Cang Li – PLoS Pathogens

Environmental Microbiome

Microbial characteristics response to the soil quality of newly created farmland on the Loess Plateau – Chen Xu – Environmental Science and Pollution Research


Human microbiome privacy risks associated with summary statistics – Jae-Chang Cho – PLoS One

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data – Achal Dhariwal – NAR Genomics and Bioinformatics

March 27, 2021

Have a nice weekend! Today, in this Digest, we have an interesting review published in Science about microbiome and cancer. We have also articles about different conditions and the effect of the microbiome in the COVID19 vaccine-based immunity. More papers about: microbiome of wild animals,  cow microbiome and glyphosate,  anorexia microbiome in a mice model, and more!

Human and General Microbiome

Review: The microbiome and human cancer – Gregory D. Sepich-Poore – Science

Alterations in mucosa-associated microbiota in the stomach of patients with gastric cancer – Yilin Deng – Cellular Oncology 

Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease – Menghan Liu – eLife

The gut microbiome in subclinical atherosclerosis: a population-based multi-phenotype analysis – Sibo Zhu – Rheumatology

The microbiome in atopic patients and potential modifications in the context of the severe acute respiratory syndrome coronavirus 2 pandemic – Euna Lee – Current Opinion in Allergy and Clinical Immunology

An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches – Claudie Lamoureux – Scientific Reports

The Role of Mucosal Immunity and Recombinant Probiotics in SARS-CoV2 Vaccine Development – Shima Moradi-kalbolandi – Probiotics and Antimicrobial Proteins

Propionate catabolism by CD-associated adherent-invasive E. coli counteracts its anti-inflammatory effect – Allison Agus – Gut Microbes

Metabolic Syndrome Cannot Mask the Changes of Fecal Microbiota Compositions Caused by Primary Hepatocellular Carcinoma – Jiajia Ni – Letters in Applied Microbiology

Mendelian Randomization Analysis Reveals Causal Effects of the Human Gut Microbiota on Abdominal Obesity – Qian Xu – The Journal of Nutrition

Animal Microbiome

Diversity and functional landscapes in the microbiota of animals in the wild – Doron Levin – Science

Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis – Marjory Xavier Rodrigues – Scientific Reports

No hints at glyphosate-induced ruminal dysbiosis in cows – Fabian Billenkamp – npj Biofilms and Microbiomes 

Animal Models

Gut microbial communities from patients with anorexia nervosa do not influence body weight in recipient germ-free mice – Elaine M. Glenny – Gut Microbes

Environmental Microbiome

Invasive freshwater snails form novel microbial relationships – Laura Bankers – Evolutionary Applications

Preprint: Diversity and metagenome analysis of a hydrocarbon-degrading bacterial consortium from asphalt lakes located in Wietze, Germany – Michael O. Eze – Biorxiv

Built Environment

The Impacts of the Occupants on the Bacterial Communities of Classrooms – Zhou Feng – Current Microbiology 


Meta-analysis methods for multiple related markers: Applications to microbiome studies with the results on multiple α-diversity indices – Hyunwook Koh – Statistics in Medicine

March 20, 2021

Have a nice weekend! Today we have to remark a Free webinar to be online next March 24. We also have a bunch of articles about different beneficial compounds, microbes, or interventions on the microbiome (from human milk to dietary supplements). Today we also highlight articles about the potential effect of resident bacteria on opportunistic respiratory infections, a set of papers about insect microbiome, and a review about the use of Machine Learning in microbiome studies.


Free webinar: The One You Feed: Identifying Specific Interactions Of Dietary Fiber Structures And The Microbiota That Ferment Them. March 24, 1:30-2:30 ET

Human and General Microbiome

Parasites, niche modification, and the host microbiome: A field survey of multiple parasites – Kayleigh R. O’Keeffe – Molecular Ecology

Large-scale functional network connectivity mediate the associations of gut microbiota with sleep quality and executive functions – Huanhuan Cai – Human Brain Mapping

Early Life Microbiome

Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial – Clara Yieh Lin Chong – Frontiers in Cellular and Infection Microbiology

Respiratory Tract Microbiome

Resident bacteria contribute to opportunistic infections of the respiratory tract – Yifan Wu – PLoS Pathogens

The influence of nasal microbiome diversity and inflammatory patterns on the prognosis of nasal polyps – Weigang Gan – Scientific Reports

Animal Microbiome

Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation – Anita Silver – PLoS One

Pollinators mediate floral microbial diversity and network under agrochemical disturbance – Na Wei – Molecular Ecology

Assessment of bacterial and fungal populations in urine from clinically healthy dogs using next-generation sequencing – Tonatiuh Melgarejo – Journal of Veterinary Internal Medicine

Immunosuppressive effect of mesenchymal stem cells on lung and gut CD8 + T cells in lipopolysaccharide-induced acute lung injury in mice – Yanping Xu – Cell Proliferation

Environmental Microbiome

Aerobiological study of bacterial and fungal community composition in the atmosphere of Mexico City throughout an annual cycle – María del Carmen Calderón-Ezquerro – Environmental Pollution

Beneficial Microbes and Compounds

Bio-therapeutics from Human Milk: Prospects and Perspectives – Kumar Siddharth Singh – Journal of Applied Microbiology

Low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diet compared with traditional dietary advice for diarrhea-predominant irritable bowel syndrome: a parallel-group, randomized controlled trial with analysis of clinical and microbiological factors associated with patient outcomes – Yawen Zhang – The American Journal of Clinical Nutrition

Synergistic Protective Effects of Different Dietary Supplements Against Type 2 Diabetes via Regulating Gut Microbiota – Leilei Yu – Journal of Medicinal Food

Characterization of antibacterial activity of a N-acetylmuramoyl-L-alanine amidase produced by Latilactobacillus sakei isolated from salami – Adriana Lopez-Arvizu – World Journal of Microbiology and Biotechnology 

Administration of β-lactam antibiotics and delivery method correlate with intestinal abundances of Bifidobacteria and Bacteroides in early infancy, in Japan – Naruaki Imoto – Scientific Reports

Lactobacillus acidophilus LA5 improves saturated fat-induced obesity mouse model through the enhanced intestinal Akkermansia muciniphila – Thunnicha Ondee – Scientific Reports

Plant Microbiome

Review: Linking Plant Secondary Metabolites and Plant Microbiomes: A Review – Zhiqiang Pang – Frontiers in Plant Science


Review: Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment – Laura Judith Marcos-Zambrano – Frontiers in Microbiology

December 30, 2020

Have a good day! Greetings from Santiago, Chile.  Today, in this Digest: a set of papers about the microbiome-gut-brain axis, as well as a couple of studies about vaginal microbiota. We have also some articles about the microbiome of dogs and turtles, as well as a study about the relationship between microplastic and shrimp microbiota. Finally, we have also some articles about new tools for microbiome analysis, and best practices for developing microbiomics methods.

P.S.: As a member of the MD Team, I want to wish Dr. Bik and all the other members of the Team, a Happy New Year, hoping this 2021 could be much better than this challenging 2020. 

And, of course, thanks to everyone who visits us and share our posts! Happy New Year!

Human and General Microbiome

Review: The intervention of unique plant polysaccharides – Dietary fiber on depression from the gut-brain axis – Ying Sun  – International Journal of Biological Macromolecules

Review: Effects of Metformin on the Gut Microbiota in Obesity and Type 2 Diabetes Mellitus –  Zhang and Hu – Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy 

Review: Microbiota-Gut-Brain Axis as a Regulator of Reward Processes – Rubén García‐Cabrerizo – Journal of Neurochemistry

Review: Gut microbiota and systemic immunity in health and disease – Bernard C Lo – International Immunology

The alteration and potential relationship of vaginal microbiota and chemokines for unexplained recurrent spontaneous abortion – Fan, Tao MM – Medicine

Oral microbiota and atherothrombotic carotid plaque vulnerability in periodontitis patients. A cross-sectional study – Adrian Brun – Journal of Periodontal Research

Comparison of the vaginal microbiota in postmenopausal Black and White women – Patricia L Hudson – The Journal of Infectious Diseases

Effect of storage, temperature, and extraction kit on the phylogenetic composition detected in the human milk microbiota – Katriona E. Lyons – MicrobiologyOpen

Gut Microbiome Profile After Pancreatectomy in Infants With Congenital Hyperinsulinism – Mary Ellen  Vajravelu – Pancreas 

The beneficial or detrimental fluoride to gut microbiota depends on its dosages – Guijie Chen – Ecotoxicology and Environmental Safety

A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen – Anilei Hoare – The ISME Journal 

Model and non-model animal microbiome

Neutrophil elastase inhibitor (MPH-966) improves intestinal mucosal damage and gut microbiota in a mouse model of 5-fluorouracil-induced intestinal mucositis – Kung-Ju Chen – Biomedicine & Pharmacotherapy

Graded Dietary Resistant Starch Concentrations on Apparent Total Tract Macronutrient Digestibility and Fecal Fermentative End-Products and Microbial Populations of Healthy Adult Dogs – Alison N Beloshapka – Journal of Animal Science

Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta) – Matthew Parks – PLoS One

A preliminary study of the association between colonization of microorganism on microplastics and intestinal microbiota in shrimp under natural conditions – Muting Yan –  Journal of Hazardous Materials

Into the sea: Antimicrobial resistance determinants in the microbiota of little penguins (Eudyptula minor) – Ida C. Lundbäck – Infection, Genetics and Evolution 

Other Microbiome studies

Microbiome Yarns: bacterial predators, tissue tropism and molecular decoys – Kenneth Timmis – Microbial Biotechnology

Microbiota succession during aerobic stability of maize silage inoculated with Lentilactobacillus buchneri NCIMB 40788 and Lentilactobacillus hilgardii CNCM-I-4785 – Pascal Drouin – MicrobiologyOpen

Temporal and spatial interactions modulate the soybean microbiome – Itumeleng Moroenyane – FEMS Microbiology Ecology (Itumeleng is a past member of the MD Team)

Bioinformatics and Microbiome Analysis

Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods – Nicholas A.Bokulich – Computational and Structural Biotechnology Journal 

Metage2Metabo, microbiota-scale metabolic complementarity for the identication of key species – Arnaud Belcour – eLife

Compositional zero-inflated network estimation for microbiome data – Min Jin Ha – BMC Bioinformatics

December 11, 2020

Have a nice Friday! In this Digest: Fecal microbiota transplant and its impact on immunotherapy-refractory melanoma patients, different reviews about microbiome and COVID19, Obesity and Diabetes; lung microbiome, microbiome relationship with vitamin D; additionally, microbiota studies in sponges, wolves, mosquitos and other animals; finally, we have a set of papers on soil microbiome and a couple of papers covering methods in microbiome sequencing and analysis.    

Human and General Microbiome

Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients – Erez N. Baruch – Science

Utilizing microbiome approaches to assist source tracking, treatment and prevention of COVID-19: Review and assessment – Maozhen Han – Computational and Structural Biotechnology Journal 

Microbiota Transplant in the Treatment of Obesity and Diabetes: Current and Future Perspectives – Michael Napolitano – Frontiers in Microbiology

The potential role of vitamin D supplementation as a gut microbiota modifier in healthy individuals – Parul Singh – Scientific Reports

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors – Vladimir A. Veselovsky – Frontiers in Immunology

Microbiome dysbiosis in lung cancer: from composition to therapy – Ning-Ning Liu – npj Precision Oncology 

Strain diversity in the microbiome: Lessons from Bacteroides fragilis – Hannah C. Carrow – PLoS Pathogens 

Bacterial and fungal profiles as markers of infliximab drug response in inflammatory bowel disease – Rebecka Ventin-Holmberg – Journal of Crohn’s and Colitis

Response to faecal microbiota transplantation in ulcerative colitis is not sustained long term following induction therapy – Craig Haifer – Gut (BMJ)

The respiratory microbiota during and following mechanical ventilation for respiratory infections in children – Emma M. de Koff – European Respiratory Journal

Increasing levels of Parasutterella in the gut microbiome correlate with improving low-density lipoprotein levels in healthy adults consuming resistant potato starch during a randomised trial – Jason R. Bush – BMC Nutrition

Preview: Fiber Sets up the Battleground for Intestinal Prevotella – Meng Wu – Cell Host and Microbe

Animal Microbiome

Preprint: Family matters: The genomes of conserved bacterial symbionts provide insight into specialized metabolic relationships with their sponge host – Samantha C Waterworth – BioXriv

Gut Microbiomes Differ Among Dietary Types and Stool Consistency in the Captive Red Wolf ( Canis rufus) – Morgan Bragg – Frontiers in Microbiology

A core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis – Davide Porcellato – Scientific Reports

Relative contributions of various endogenous and exogenous factors to the mosquito microbiota – Haikel N. Bogale, – Parasites & Vectors

A Cross-Sectional Study of Dairy Cattle Metagenomes Reveals Increased Antimicrobial Resistance in Animals Farmed in a Heavy Metal Contaminated Environment – Natalia Carrillo Gaeta – Frontiers in Microbiology 

Intestine Bacterial Community Composition of Shrimp Varies Under Low- and High-Salinity Culture Conditions – Dongwei Hou –  Frontiers in Microbiology

Host miRNA-21 promotes liver dysfunction by targeting small intestinal Lactobacillus in mice – André A. Santos – Gut Microbes 

Beneficial Microbes and Compounds

Probiotic Lactobacillus fermentum strain JDFM216 improves cognitive behavior and modulates immune response with gut microbiota – Mi Ri Park – Scientific Reports

Plasmid Vectors for in Vivo Selection-Free Use with the Probiotic E. coli Nissle 1917 – Anton Kan – ACS Synthetic Biology

Purple-leaf tea (Camellia sinensis L.) ameliorates high-fat diet induced obesity and metabolic disorder through the modulation of the gut microbiota in mice – Yu-Chun Lin – BMC Complementary Medicine and Therapies

Plant and Soil Microbiome

In Situ Rhizosphere Microbiome in Antarctic Vascular Plants, Modulated by Soil Condition – Claudia Rabert – Microbiology Resource Announcements

Dazomet application suppressed watermelon wilt by the altered soil microbial community – Feiying Zhu – Scientific Reports

Case Study upon Foliar Application of Biofertilizers Affecting Microbial Biomass and Enzyme Activity in Soil and Yield Related Properties of Maize and Wheat Grains – Dragana Latkovic – biology

Biostimulating effect of L-tryptophan on the yield and chemical and microbiological quality of perennial ryegrass (Lolium perenne) herbage and silage for ruminant – Sebastian Wojciech Przemieniecki – Journal of the Science of Food and Agriculture


Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome – Min Yap – Scientific Reports

Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data – Julie Chih-yu Chen – Biology Direct

November 28, 2020

Greetings from Santiago, Chile! Today, in this brief Digest, we have a preprint with interesting results obtained by the Dutch Microbiome Project. We have as well a couple of papers exploring the relationship between microbiome and COVID-19, and more other papers. Have a nice weekend!

Human and General Microbiome

Preprint: The Dutch Microbiome Project defines factors that shape the healthy gut microbiome – Ranko Gacesa – BioRxiv

Viral Infection-Induced Gut Dysbiosis, Neuroinflammation, and α-Synuclein Aggregation: Updates and Perspectives on COVID-19 and Neurodegenerative Disorders – Cristian Follmer – ACS Chemical Neuroscience

Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19 – Taha Baghbani – Microbial Cell Factories

Gut microbiome is more stable in males than in females during the development of colorectal cancer – Haijun Liao – Journal of Applied Microbiology

Expression of toll-like and adhesive receptors on epithelial cells of the oral mucosa in periodontitis – O.A. Lukova – Russian Clinical Laboratory Diagnostics

The Microbiome in Hidradenitis Suppurativa: A Review – Kirsty J. L. Wark – Dermatology and Therapy 

Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes – Meghan H. Shilts – Scientific Reports 

Emotional well-being and gut microbiome profiles by enterotype – Sung-Ha Lee – Scientific Reports 

Vitamin D metabolites and the gut microbiome in older men – Robert L. Thomas – Nature Communications

Animal Microbiome

Reduced rotavirus vaccine efficacy in protein malnourished human-faecal-microbiota-transplanted gnotobiotic pig model is in part attributed to the gut microbiota – V. Srivastava – Beneficial Microbes

Clinical efficacy of spray-based heat-treated lactobacilli in canine atopic dermatitis: a preliminary, open-label, uncontrolled study – Domenico Santoro – Veterinary Dermatology


Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern – Varun Paul – Scientific Reports 

Microbiome Methods and Analysis

The application potential of machine learning and genomics for understanding natural product diversity, chemistry, and therapeutic translatability – David Prihoda – Natural Product Reports


Efficient protection of microorganisms for delivery to the intestinal tract by cellulose sulphate encapsulation – Walter H. Gunzburg – Microbial Cell Factories

November 19, 2020

Today, in this (late) Digest:  a set of reviews about the role of microbiota in neurodegeneration, psoriasis and stroke; different studies about the microbiome genital/urinary tracts, and microbiome studies in pandas, salmon and pigeons.

Human and General Microbiome

Review: Complex Interaction between Resident Microbiota and Misfolded Proteins: Role in Neuroinflammation and Neurodegeneration – Juliana González-Sanmiguel – Cells (MDPI)

Review: Gut-Brain-Skin Axis in Psoriasis: A Review – Guang Chen – Dermatology and Therapy

Minireview: The Gut Ecosystem: A Critical Player in Stroke – Rosa Delgado Jiménez – NeuroMolecular Medicine

Meta-analysis: A meta-analysis of the effect of binge drinking on the oral microbiome and its relation to Alzheimer’s disease – Ayuni Yussof – Scientific Reports

Associations between Pro- and Anti-Inflammatory Gastro-Intestinal Microbiota, Diet, and Cognitive Functioning in Dutch Healthy Older Adults: The NU-AGE Study – Annick P. M. van Soest – Nutrients (MDPI)

Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery – Marina Muñoz – Microbial Genomics

Exogenous infusion of short-chain fatty acids can improve intestinal functions independently of the gut microbiota – Hua Zhou – Journal of Animal Science

The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study – N. V. Patin – mBio

Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota – Nesreen H Aljahdali – BMC Microbiology

Fusobacterium nucleatum in biopsied tissues from colorectal cancer patients and alcohol consumption in Korea – Myungsook Kim – Scientific Reports

The Gut Microbiome in Polycystic Ovary Syndrome and its Association with Metabolic Traits – Kreete Lüll – The Journal of Clinical Endocrinology & Metabolism

Genito-Urinary Tract Microbiome

The discovery of bacterial biofilm in patients with muscle invasive bladder cancer – Naomi Nadler – APMIS

Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection – Bi Qingqing – Microbial Pathogenesis

Ureteral Stent Microbiota Is Associated with Patient Comorbidities but Not Antibiotic Exposure – Kait F. Al – Cell Reports Medicine

Beneficial Microbes and Compounds

Review: Living Therapeutics: The Next Frontier of Precision Medicine – Vince W. Kelly – ACS Synthetic Biology

Interplay between dietary phenolic compound intake and the human gut microbiome in hypertension: A cross-sectional study – Lorena Calderón-Pérez – Food Chemistry 

Blueberry Consumption Challenges Hepatic Mitochondrial Bioenergetics and Elicits Transcriptomics Reprogramming in Healthy Wistar Rats – Sara Nunes – Pharmaceutics (MDPI)

Lactobacillus reuteri DSM 17938 alleviates d-galactosamine-induced liver failure in rats – Huiyong Jiang – Biomedicine & Pharmacotherapy

Animal Microbiome

Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice – Artem P. Gureev – PLoS One

Changes in the diversity and composition of gut microbiota in pigeon squabs infected with Trichomonas gallinae – Feng Ji – Scientific Reports

Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing – Lan Zhang – Microbiology Open

Association of gut microbiota with metabolism in juvenile Atlantic salmon – H. Dvergedal – Microbiome 

Food Microbiome

Differentiation of Milk and Whey Protein Concentrates by Microbiome Profiling Using 16S Metagenomics – Christopher M Thompson – Journal of AOAC international

Microbiome analysis methods and tools

Mediation effect selection in high-dimensional and compositional microbiome data – Haixiang Zhang – Statistics in Medicine

Evaluation of Sampling Methods for the Study of Avian Respiratory Microbiota – Michael Edward C. Abundo – Avian Diseases

MHSNMF: multi-view hessian regularization based symmetric nonnegative matrix factorization for microbiome data analysis – Yuanyuan Ma – BMC Bioinformatics

November 13, 2020

Have a nice Friday! Today, in this Digest, a study published in Nature showing exciting associations between the microbiome and the human serum metabolome; we also have different papers about different respiratory system health conditions, different paediatric studies, and studies on the microbiome in different genitourinary health conditions. It is worth to highlight as well another study (Ford et al., Molecular Biology and Evolution) about how in vivo microbiome coevolution can influence host immunity.

Human and General Microbiome

Review: The gut microbiome as a target for adjuvant therapy in obstructive sleep apnea – Mohammad Badran – Expert Opinion on Therapeutic Targets

Review: The microbiome, genetics, and gastrointestinal neoplasms: the evolving field of molecular pathological epidemiology to analyze the tumor-immune-microbiome interaction – Kosuke Mima – Human Genetics 

Review: Faecal microbiota transplantation: what’s beyond Clostridium difficile infection? – Aravind Gokula Tamilarasan – European Journal of Gastroenterology & Hepatology 

Review: A bridge for short-chain fatty acids to affect inflammatory bowel disease, type 1 diabetes, and non-alcoholic fatty liver disease positively: by changing gut barrier – Wangxin Liu – European Journal of Nutrition

A reference map of potential determinants for the human serum metabolome – Noam Bar – Nature

Commentary: Building a chemical blueprint for human blood – Patrick H. Bradley & Katherine S. Pollard

In vivo microbial coevolution favours host protection and plastic downregulation of immunity – Suzanne A Ford – Molecular Biology and Evolution

Mucin-Degrading Microbes Release Monosaccharides That Chemoattract Clostridioides difficile and Facilitate Colonization of the Human Intestinal Mucus Layer – Melinda A. Engevik – ACS Infectious Diseases

The gut microbiome drives inter- and intra-individual differences in metabolism of bioactive small molecules – Asimina Kerimi – Scientific Reports

Gut Microbiota Changes and Their Relationship with Inflammation in Patients with Acute and Chronic Insomnia –  Li Y – Dovepress 

Microbiome and Respiratory System Health

Lower airway dysbiosis affects lung cancer progression – Jun-Chieh J Tsay – Cancer Discovery

Variations in fecal microbial profiles of acute exacerbation and stable-state chronic obstructive pulmonary disease – Yonghong Wu – Life Sciences

Correlation between adenotonsillar microbiome and clinical characteristics of pediatrics with snoring – Kyung Soo Kim – Clinical and Experimental Otorhinolaryngology 

Microbiome and Paediatrics

Delivery mode and gut microbial changes correlate with an increased risk of childhood asthma – Jakob Stokholm – Science Translational Medicine

Intestinal Microbiota in Children With Symptomatic Dientamoeba fragilis Infection: A Case-control Study – Michael W. van Kalleveen – The Pediatric Infectious Disease Journal

Genito-urinary Tract Microbiome

Influence of dapivirine vaginal ring use on cervicovaginal immunity and functional microbiome in adolescent girls – Christina Farr Zuend – AIDS

Bare Versus Hair: Do Pubic Hair Grooming Preferences Dictate the Urogenital Microbiome? – Julia Geynisman-Tan – Female Pelvic Medicine & Reconstructive Surgery

Beneficial Microbes and Compounds

A polysaccharide from Fagopyrum esculentum Moench bee pollen alleviates microbiota dysbiosis to improve intestinal barrier function in antibiotic-treated mice – Liuying Zhu – Food and Function

Phytogenic products, used as alternatives to antibiotic growth promoters, modify the intestinal microbiota derived from a range of production systems: an in vitro model – Yadav S. Bajagai – Applied Microbiology and Biotechnology

COVID-19 and Microbiota

COVID-19 in the Developing World: Is the Immune Response to α-Gal an Overlooked Factor Mitigating the Severity of Infection? – Adnan Hodžić – ACS Infectious Diseases

Animal Microbiome / Animal Models

Effects of Vitamin D3 on Intestinal Flora in a Mouse Model of Inflammatory Bowel Disease Treated with Rifaximin – Zijun Gu – Medical Science Monitor

Gut microbiota depletion by chronic antibiotic treatment alters the sleep/wake architecture and sleep EEG power spectra in mice – Yukino Ogawa – Scientific Reports

Comparison of different modes of antibiotic delivery on gut microbiota depletion efficiency and body composition in mouse – Pauline Tirelle – BMC Microbiology

Plant Microbiome

Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance – Melanie Maria Obermeier – The ISME Journal


A network-based approach to deciphering a dynamic microbiome’s response to a subtle perturbation – Grace Tzun-Wen Shaw – Scientific Reports

A comprehensive investigation of metagenome assembly by linked-read sequencing – Lu Zhang – Microbiome (BMC)

Light-Activated Electron Transfer and Catalytic Mechanism of Carnitine Oxidation by Rieske-type Oxygenase from Human Microbiota – Muralidharan Shanmugam – Angewandte Chemie

Microbial communities and gene contributions in smokeless tobacco products – A. J. Rivera – Applied Microbiology and Biotechnology

November 6, 2020

Shalom from Israel!

While the eyes of the world are looking at the US elections results, it’s good to know that the world of microbiome research is stable and produces great scientific discoveries. So stop refreshing the news websites, grab yourself a cup of cofee and enjoy your Saturday.

Today’s digest has some great papers about memory in microboimes, factors that shapes bacterial growth, infant skin microbial communities, degraded soils restoration using self-assembly communities, songbirds microbiome, antiSMASH3 is out (!), useful youtube video for metagenome ML analysis in MATLAB and more. Reminding those of you who are intrested in agriculture-related microbioe studies to stop by and follow my bot agmicroPapers

General microbiology

Memory shapes microbial populations, Chaitanya S Gokhale , bioRxiv

Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness, Emily C. Pierce, Nature Microbiology

Environmental and Physiological Factors Affecting High-Throughput Measurements of Bacterial Growth, Esha Atolia , mBio

Human microbiome

Host variables confound gut microbiota studies of human disease, Ivan Vujkovic-Cvijin, Nature

Infant Skin Bacterial Communities Vary by Skin Site and Infant
Age across Populations in Mexico and the United States
, Melissa B. Manus, mSystems

Plant and soil microbiome

Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins, Nick C. Snelders, Nature Plants

Assembly and variation of root-associated microbiota of rice during their vegetative growth phase with and without lindane pollutant, Jiayin Feng, Soil Ecology Letters

Restoring degraded microbiome function with self-assembled communities, Carlos Fernando Gutierrez Landazuri , FEMS Micro. Eco.

Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant – microbiome – soil continuum, Myrto Tsiknia, FEMS Micro. Eco.

Animal microbiome

Evidence supporting the microbiota–gut–brain axis in a songbird, Morgan C. Slevin, Biology Letters

Comparative Analysis of the Fecal Microbiota of Wild and Captive Beal’s Eyed Turtle (Sacalia bealei) by 16S rRNA Gene Sequencing, Jonathan J. Fong , Front. Micro.

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests, Markus Oberpaul , Front. Micro.


EUKulele: Taxonomic annotation of the unsung
eukaryotic microbes
, Arianna I. Krinos, JOSS

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes, Kai Blin, Nucleic Acids Research

**Youtube Video- Microbiome: How to Navigate Through Matlab to Perform Machine Learning Analysis on Metagenomics Data

**Help questionnaire! Natural Products – Data Repositories Questionnaire