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

October 24, 2020

Greetings from Santiago, Chile! Today, in this Digest we have several reviews about microbiota and different conditions or interventions. We have also papers about the microbial evolution and its relationship with the host, the role of O-glycosylated mucus, the microbiome of neonates and the influence of probiotics, and more…    

Human and General Microbiome

Review: The gut microbiota-brain axis in behaviour and brain disorders – Livia H. Morais – Nature Reviews Microbiology

Review: Gut microbiota in pancreatic diseases: possible new therapeutic strategies – Li-long Pan – Acta Pharmacologica Sinica 

Review: The Gut Microbiome and the Triple Environmental Hit Concept of Inflammatory Bowel Disease Pathogenesis – Richard Kellermayer – Journal of Pediatric Gastroenterology and Nutrition

Review: Allogenic stem cell transplant-associated acute graft versus host disease: a computational drug discovery text mining approach using oral and gut microbiome signatures – M. F. Beckman – Supportive Care in Cancer 

Experimental evolution makes microbes more cooperative with their local host genotype – Rebecca T. Batstone – Science

Proximal colon-derived O-glycosylated mucus encapsulates and modulates the microbiota – Kirk Bergstrom – Science

The Microbiota Profile in Inflamed and Non-Inflamed Ileal Pouch-Anal Anastomosis – Sabrina Just Kousgaard – Microorganisms (MDPI)

Altered Gut Microbiome and Environmental Factors Associated with Development of Eczema in Hong Kong Infants: A 4-Month Pilot Study – Carmen Wing Han Chan – International Journal of Environmental Research and Public Health

Beneficial microbes and Compounds

Systematic Review: The role of pro-, pre- and symbiotics in cancer: A systematic review – Miarons Marta – Journal of Clinical Pharmacy and Therapeutics

Review: Fiber and Prebiotic Interventions in Pediatric Inflammatory Bowel Disease: What Role Does the Gut Microbiome Play? – Genelle R. Healey – Nutrients (MDPI)

Influence of probiotic supplementation on the developing microbiota in human preterm neonates – Niels van Best – Gut Microbes

Anti-Inflammatory and Intestinal Microbiota Modulation Properties of Jinxiang Garlic ( Allium sativum L.) Polysaccharides toward Dextran Sodium Sulfate-Induced Colitis – Xin Shao – Journal of Agricultural and Food Chemistry

Food Microbiome

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China – YiMing Li – Scientific Reports

Animal Microbiome

Review: Toxin Degradation by Rumen Microorganisms: A Review – Zhi Hung Loh – Toxins (MDPI)

Gut dysbiosis associated with the rats’ responses in methamphetamine-induced conditioned place preference – Cheng Yang – Addiction Biology

A High-Fat Diet Increases Gut Microbiota Biodiversity and Energy Expenditure Due to Nutrient Difference – Botao Wang – Nutrients (MDPI)

Plant Microbiome

Microbiome-wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava – Lin Zhang – Plant Biotechnology Journal

Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units – Lisa Joos – BMC Genomics


Clustering on Human Microbiome Sequencing Data: A Distance-Based Unsupervised Learning Model – Dongyang Yang – Microorganisms (MDPI)

A generalized machine-learning aided method for targeted identification of industrial enzymes from metagenome: a xylanase temperature dependence case study – Mehdi Foroozandeh Shahraki – Biotechnology and Bioengeenering

October 17, 2020

Have a nice weekend! Today, in this brief Digest, several papers about microbiome studies in animal models. Additionally, some highlighted studies in humans: the vaginal microbiota in a Swedish cohort, and the microbiota from the urinary tract, by the use of culturomics.

Human and General Microbiome

Using data science for medical decision making case: role of gut microbiome in multiple sclerosis – Jasminka Hasic Telalovic- BMC Medical Informatics and Decision Making

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut – Grégory Dubourg – Frontiers in Microbiology

Vaginal microbiota and human papillomavirus infection among young Swedish women – Liqin Cheng – npj Biofilms and Microbiomes

Review: Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities – Saad Khan – Annual Review of Pharmacology and Toxicology 

Animal Microbiome

Developmental stages in microbiota, bile acids, and clostridial species in healthy puppies – Amanda B. Blake – Journal of Veterinary Internal Medicine

Screening of Microbes Associated With Swine Growth and Fat Deposition Traits Across the Intestinal Tract – Shi Tang – Frontiers in Microbiology

Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats – Qinghong Li – Frontiers in Microbiology

Inulin alleviates adverse metabolic syndrome and regulates intestinal microbiota composition in Nile Tilapia ( Oreochromis niloticus) fed with high-carbohydrate diet – Tong Wang – British Journal of Nutrition

Minireview: Transmission of the sponge microbiome: moving towards a unified model – Bruno Francesco Rodrigues de Oliveira  – Environmental Microbiology Reports 

Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments – Sohaib H.Mazhar – Science of The Total Environment

Friend or foe? Effects of host immune activation on the gut microbiome in the caterpillar Manduca sexta – Laura E. McMillan – Journal of Experimental Biology

Environmental Microbiome

Correspondence: Towards meaningful scales in ecosystem microbiome research – Francisco Dini‐Andreote – Environmental Microbiology

Preprint: Genomics-accelerated discovery of diverse fungicidal bacteria – Matthew B Biggs – BioXriv

Preprint: Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics – Tom O. Delmont – BioXriv

Beneficial Microbes and Compounds

The chemopreventive effects of Huangqin-tea against AOM-induced preneoplastic colonic aberrant crypt foci in rats and omics analysis – Jie Shen – Food & Function

Prophylactic effects of oral administration of Lactobacillus casei on house dust mite-induced asthma in mice – Lingzhi Li – Food & Function

Lactobacillus plantarum Shinshu N-07 isolated from fermented Brassica rapa L. attenuates visceral fat accumulation induced by high-fat diet in mice – T. Yin – Beneficial Microbes

September 19, 2020

Have a nice weekend! Today, in this digest: a pair of papers released in Science, showing interesting results about the dialogue between the microbiota and the host. In Mager et al., the study showed that inosine, a metabolite released by microbes, may have an adjuvant role in cancer immune treatment. In the Lobel et al. paper, they demostrated that “diet can tune microbiota function to support healthy host physiology through posttranslational modification without altering microbial community composition”.

And of course, there are more papers 🙂 

Human and General Microbiome

Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy – Lukas F. Mager – Science

> Perspective about this paper: Messengers from the microbiota – Fyza Y. Shaikh 

Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function – Lior Lobel – Science 

>  Perspective about this paper: The gut microbiota in kidney disease – Jennifer L. Pluznick

Fecal microbiota transplantation in inflammatory bowel disease patients: A systematic review and meta-analysis – Luciane de Fátima Caldeira – Plos One

Minireview: Antimicrobial peptides in the gut-brain axis: A straightforward review to unravel some missing links – Fabiano Pinheiro da Silva – Journal of Neuroscience Research

Microbiome analysis of contact lens care solutions and tear fluids of contact lens wearers: Possible involvement of streptococcal antigens in allergic symptoms related to contact lens wear – Fumika Hotta – International Journal of Molecular Medicine

Longitudinal Changes in Skin Microbiome and Microbes Associated with Change in Skin Status in Patients with Psoriasis – Hailun Wang – Acta Dermato Venereologica

Changes in fecal short-chain fatty acids following fecal microbiota transplantation in patients with irritable bowel syndrome – Magdy El‐Salhy – Neurogastroenterology and Motility

Analysis of airway microbiota in adults from a Brazilian cystic fibrosis center – Cassiana Costa Ferreira Leite – Brazilian Journal of Microbiology

Bacterial diversity and inflammatory response at first-time visit in younger and older individuals with diabetic foot infection (DFI) – Stefan Dörr – Acta Diabetologica 

Animal Microbiome

Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal – Jiakuo Yan – AMB Express

The Gut Microbial Community Structure of the North American River Otter (Lontra canadensis) in the Alberta Oil Sands Region in Canada: Relationship with Local Environmental Variables and Metal Body Burden – Galen Guo – Environmental Toxicology and Chemistry

Dynamic changes of the fecal bacterial community in dairy cows during early lactation – Shuai Huang – AMB Express

Comparative analysis of the pulmonary microbiome in healthy and diseased pigs – Zongjie Li – Molecular Genetics and Genomics

Plant microbiome

Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities – Barbara A. Methe – Plos One

Microbiome and diet

Minireview: Soy bioactive peptides and the gut microbiota modulation – Tolulope Joshua Ashaolu – Applied Microbiology and Biotechnology 

September 16, 2020

Greetings from Chile! Today, in this Digest, it is worth to highlight: a study showing associations between the use of antibiotics and the risk of appendicitis, a review about microbiota and colorectal cancer (CRC) risk and another review about markers for diabetes-associated chronic kidney disease. In addition, there are a set of papers about microbiome changes under short- and long-term antibiotic use in the animal lab, and microbiota changes in the treatment of non-model animals, such as the sika deer.   

Human Microbiome

Antibiotics during childhood and development of appendicitis-a nationwide cohort study – Jacob Antonsen – Alimentary Pharmacology and Therapeutics

Review: Bacteria-related changes in host DNA methylation and the risk for CRC – Iradj Sobhani – Gut Microbes

Review: Potential for Novel Biomarkers in Diabetes-Associated Chronic Kidney Disease: Epigenome, Metabolome, and Gut Microbiome – Ashani Lecamwasam – Biomedicines

Microbiota-Mitochondria Inter-Talk: A Potential Therapeutic Strategy in Obesity and Type 2 Diabetes – Teresa Vezza – Antioxidants

Preprint: Impact of sleep fragmentation, heart failure, and their combination, on the gut microbiome – Olfat Khannous-Lleiffe – BioRxiv

Microbiome and Diet

Relative abundance of the Prevotella genus within the human gut microbiota of elderly volunteers determines the inter-individual responses to dietary supplementation with wheat bran arabinoxylan-oligosaccharides – Wing Sun Faith Chung – BMC Microbiology

Animal Microbiome

Acute and long-term effects of antibiotics commonly used in laboratory animal medicine on the fecal microbiota – Scott W. Korte – Veterinary Research

The impact of anthelmintic treatment on gut bacterial and fungal communities in diagnosed parasite-free sika deer Cervus nippon – Xiaolong Hu – Applied genetics and molecular biotechnology

On the way to specificity – Microbiome reflects sponge genetic cluster primarily in highly structured populations – Cristina Díez‐Vives – Molecular Ecology

The gut microbiota may be a novel pathogenic mechanism in loosening of orthopedic implants in rats – Meghan M. Moran – The FASEB Journal

Characterization of Gut Microbiota in Prenatal Cold Stress Offspring Rats by 16S rRNA Sequencing – Jiasan Zheng – Animals

Obesity Worsens Gulf War Illness Symptom Persistence Pathology by Linking Altered Gut Microbiome Species to Long-Term Gastrointestinal, Hepatic, and Neuronal Inflammation in a Mouse Model – Dipro Bose – Nutrients

Beneficial Microbes and Compounds

Influence of a cholesterol-lowering strain Lactobacillus plantarum LP3 isolated from traditional fermented yak milk on gut bacterial microbiota and metabolome of rats fed with a high-fat diet – Zitong Ding – Food and Function

The Microbiota-Derived Metabolite of Quercetin, 3,4-Dihydroxyphenylacetic Acid Prevents Malignant Transformation and Mitochondrial Dysfunction Induced by Hemin in Colon Cancer and Normal Colon Epithelia Cell Lines – Mabel Catalán – Molecules


Constructing bi-plots for random forest: Tutorial – Lionel Blanchet – Analytica Chimica Acta

More Microbes

Cultural isolation of spore-forming bacteria in human feces using bile acids – Masaru Tanaka – Scientific Reports

Bed bugs shape the indoor microbial community composition of infested homes – Madhavi L. Kakumanu – Science of The Total Environment