October 21, 2018

Today’s microbiome digest highlights more about the diet-microbiome and brain functions, the role of microbiome in oral mucosal immunopathology and the microbiomes from mink, beetles, and turkey. Enjoy reading!

 General microbiome

Review: Complex Feed-Forward and Feed-Back Mechanisms Underlie the Relationship Between Traumatic Brain Injury and the Gut–Microbiota–Brain Axis – T. Tyler Patterson – Shock

Microbial community shifts in biogas reactors upon complete or partial ammonia inhibition – Zuopeng Lv – Applied Microbiology and Biotechnology

Review: How Can We Define “Optimal Microbiota?”: A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture – Wakako Ikeda-Ohtsubo – Frontiers in Nutrition

A dysbiotic microbiome triggers TH17 cells to mediate oral mucosal immunopathology in mice and humans – Nicolas Dutzan – Science Translational Medicine

Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products – Zhengyao Xue – mSphere

Human gut microbiome

Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women – Eveliina Munukka – Frontiers in Microbiology

Altered bile acid profile associates with cognitive impairment in Alzheimer’s disease—An emerging role for gut microbiome – Siamak MahmoudianDehkordi – Alzheimers and Dementia

Gut Dysbiosis And Paediatric Crohn’s Disease – Andrea Brusaferro – Journal of Infection

Oral Administration of Porphyromonas gingivalis Alters the Gut Microbiome and Serum Metabolome – Tamotsu Kato – mSphere

Gut Microbes May Account for the Anti-Seizure Effects of the Ketogenic Diet
Tracy Hampton – JAMA

Animal Microbiome

Investigation of the viral and bacterial microbiota in intestinal samples from mink (Neovison vison) with pre-weaning diarrhea syndrome using next generation sequencing – Julie Melsted Birch – PLOS ONE

Gut bacterial and fungal communities in ground-dwelling beetles are associated with host food habit and habitat – Rina Kudo – The ISME Journal

Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts – Brittany Forkus – Scientific Reports

Animal experiments

Gut microbiota–derived D-serine protects against acute kidney injury – Yusuke Nakade – JCI insight

Plant, root, and soil microbiome

Unraveling microbial communities associated with methylmercury production in paddy soils – Yurong Liu – Environmental Science and Technology

Changes in the Fungal Microbiome of Maize During Hermetic Storage in the United States and Kenya – Brett Lane – Frontiers in Microbiology

Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production – DaniellaGallagher – Bioresource Technology


A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping – Kazuhiro Ogai – Frontiers in Microbiology

Microbes in news

3.7 Billion-Year-Old Fossil Evidence of Microbes Disputed



October 20, 2018

Today’s microbiome digest will cover various interesting papers including effect of metformin in the shaping the gut microbiome, dysregulated microbial fermentation of soluble fibers, gut microbiome dynamics of travelers, relationship between gut microbiome and cancer immunotherapy, role of gut microbiome on drug metabolism, microbiome of healthy and dandruff scalp from Indian population and supplementation with Lactobacillus plantarumJM113, Bacillus subtilis DSM 32315 in broiler chickens. Enjoy reading.

General microbiome

Chapter: Brain–Gut Axis: Clinical Implications – JulieKhlevner – Gastroenterology Clinics of North America

Pleiotropic effects of metformin: Shaping the microbiome to manage type 2 diabetes and postpone ageing – FrancescoPrattichizzo – Ageing Research Reviews

Gut Microbiome in Obesity, Metabolic Syndrome, and Diabetes – Xinpu Chen – Current Diabetes Reports

Human gut microbiome

The Activity of Urolithin A and M4 Valerolactone, Colonic Microbiota Metabolites of Polyphenols, in a Prostate Cancer In Vitro Model – Iwona J. Stanisławska – Planta Medica

Dysregulated Microbial Fermentation of Soluble Fiber Induces Cholestatic Liver Cancer – Vishal Singh – Cell

Gut microbiota dynamics in travelers returning from India colonized with extended-spectrum cephalosporin-resistant Enterobacteriaceae: A longitudinal study – Joao Pires – Travel Medicine and Infectious Disease

Association between functional lactase variants and a high abundance of Bifidobacterium in the gut of healthy Japanese people – Kumico Kato – PLOS ONE

The intimate relationship between gut microbiota and cancer immunotherapy – Arielle Elkrief – Gut Microbes

Effects of Gut Microbiota on Drug Metabolism and Guidance for Rational Drug Use under Hypoxic Conditions at High Altitudes – Juanhong Zhang – Current Drug Metabolism

Reduced colonic mucin degradation in breastfed infants colonized by Bifidobacterium longum subsp. infantis EVC001 – Sercan Karav – FEBS openbio

The microbiome of Crohn’s disease aphthous ulcers – Claire L. O’Brien – Gut Pathogens

Scalp Microbiome

Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health – Rituja Saxena – Frontiers in Cellular and Infection Microbiology

Animal Microbiome

Intestinal toxicity of deoxynivalenol is limited by supplementation with Lactobacillus plantarumJM113 and consequentially altered gut microbiota in broiler chickens – Shengru Wu – Journal of Animal Science and Biotechnology

Screening of Phytophagous and Xylophagous Insects Guts Microbiota Abilities to Degrade Lignocellulose in Bioreactor – Amandine Gales – Frontiers in Microbiology

Supplemental Bacillus subtilis DSM 32315 manipulates intestinal structure and microbial composition in broiler chickens – Youbiao Ma – Scientific Reports

Animal experiments

Non-invasive continuous real-time in vivoanalysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice – José M. S. Fernández-Calleja – Scientific Reports

Evaluation of different mucosal microbiota leads to gut microbiota-based prediction of type 1 diabetes in NOD mice – Youjia Hu – Scientific Reports

September 23, 2018

In today’s microbiome digest there are several interesting papers under animal experiments using mice, drosophila, mosquito vector and Ixodes scapularis ticks microbiome. Other important studies include the sinus swabs microbiome from chronic rhinosinusitis patients, lymph node microbiome from Crohn’s disease, intestinal microbiome profiling in psoriasis patients and a review which highlight on several common pitfalls for clinicians analyzing and interpreting the microbiome data. Enjoy reading.

General microbiome

Mucin Degradation Niche as a Driver of Microbiome Composition and Akkermansia Muciniphila Abundance in a Dynamic Gut Model is Donor Independent – Van Herreweghen Florence – FEMS Microbiology Ecology 

The human mesenteric lymph node microbiome differentiates between Crohn’s disease and ulcerative colitis – Miranda G Kiernan – Journal of Crohn’s and Colitis 

Review: Microbial enterotypes in personalized nutrition and obesity management – Lars Christensen – The American Journal of Clinical Nutrition 

Nasal microbiome

Relative abundance of nasal microbiota in chronic rhinosinusitis by structured histopathology – Hannah N. Kuhar BA – International Forum of Allergy and Rhinology

Respiratory microbiome

Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children – M S Zinter – Clinical Infectious Diseases

Human gut microbiome

Review: Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians – Celeste Allaband – Clinical Gastroenterology and Hepatology

Increased relative abundance of Klebsiella pneumoniaecarbapenemase-producing Klebsiella pneumoniae within the gut microbiota is associated with risk of bloodstream infection in long-term acute care hospital patients – Teppei Shimasaki – Clinical Infectious Diseases

Intestinal microorganisms involved in colorectal cancer complicated with dyslipidosis – Shuwen Han – Cancer Biology and Therapy

Intestinal microbiota profiling and predicted metabolic dysregulation in psoriasis patients – Yi‐Ju Chen – Experimental Dermatology

Effects of products designed to modulate the gut microbiota on hyperlipidaemia – Xilong Deng – European Journal of Nutrition

Review: Bacterial antagonism in host-associated microbial communitiesLeonor García-Bayona – Science 

Meconium microbiome associates with the development of neonatal jaundice – Tianyu Dong – Clinical and Translational Gastroenterology

Animal experiments

The effects of metabolic syndrome, obesity, and the gut microbiome on load-induced osteoarthritis – Guss JD – Osteoarthritis Cartilage

Microbial Quantity Impacts Drosophila Nutrition, Development, and Lifespan – Erin S.Keebaugh – iScience

Sex Differences in Pulmonary Responses to Ozone in Mice: Role of the Microbiome – Youngji Cho – American Journal of Respiratory Cell and Molecular Biology

Short-term impacts of anthropogenic stressors on Aedes albopictus mosquito vector microbiota – Morgane Guégan – FEMS Microbiology Ecology

Effects of temperature on bacterial microbiome composition in Ixodes scapularis ticks – Santosh Thapa – MicrobiologyOpen

Intestinal anti-inflammatory effect of the probiotic Saccharomyces boulardii in DSS-induced colitis in mice: Impact on microRNAs expression and gut microbiota composition – Alba Rodríguez-Nogalesa – The Journal of Nutritional Biochemistry


Sequence clustering in bioinformatics: an empirical study – Quan Zou – Briefings in Bioinformatics


Using non‐invasive metagenomics to characterize viral communities from wildlife – Laura M. Bergner – Molecular Ecology Resources

September 16, 2018

Good morning! the publications from today’s microbiome digest covering the followings: Tick Microbiome, Chronic fatigue syndrome and alteration in the oral microbiome, CRC associated metabolites quantified from the faecal extracts, vaginal microbiome during cytolytic vaginosis, rumen and fecal bacterial community in high-production dairy cattle, and estimation of the expected variation in microbiome measurements (methodological research). Enjoy reading.

General microbiome

Thesis: Investigating the effects of the gut-associated microbial community on the growth of the eastern spruce budworm – Melbert Schwarz – Thesis

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing – Lisa Couper – Journal of Visualized Experiments: JoVE

Alcohol consumption increase susceptibility to pneumococcal pneumonia in a humanized murine HIV model mediated by intestinal dysbiosis – Derrick R.Samuelson – Alcohol 

Oral microbiome

Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function – Taiwu Wang – PLOSONE

Human gut microbiome

Metabolite quantification of faecal extracts from colorectal cancer patients and healthy controls – Gwénaëlle Le Gall – Oncotarget

Vaginal microbiome

Characterization of the vaginal microbiome during cytolytic vaginosis using high-throughput sequencing – Haihong Xu – Wiley

Animal microbiome

High-production dairy cattle exhibit different rumen and fecal bacterial community and rumen metabolite profile than low-production cattle – Yingyu Mu – MicrobiologyOpen

Characterization of the Functional Changes in Mouse Gut Microbiome Associated with Increased Akkermansia muciniphila Population Modulated by Dietary Black Raspberries – Pengcheng Tu – ACS Omega

Plant, root, and soil microbiome

Dynamics of soil respiration and microbial communities: Interactive controls of temperature and substrate quality – Rana ShahbazAli – Soil Biology and Biochemistry

Microbial community structure and functions differ between native and novel (exotic-dominated) grassland ecosystems in an 8-year experiment – Aleksandra Checinska Sielaff – Plant and Soil

Impacts of heavy metals and soil properties at a Nigerian e-waste site on soil microbial community – Bo Jiang – Journal of Hazardous Material

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing – Zhiying Li – Current Microbiology

Extreme environmental microbiome

Bacterial diversity in snow from mid-latitude mountain areas: Alps, Eastern Anatolia, Karakoram and Himalaya – Roberto Sergio AZZONI – Annals of Glaciology

Water and extremophile microbiome

Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake – Jian Cai – Environmental Science and Pollution Research

Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China – Hua Zhang – Ecotoxicology and Environmental Safety


Machine learning analysis of microbial flow cytometry data from nanoparticles, antibiotics and carbon sources perturbed anaerobic microbiomes – Abhishek S. Dhoble – Journal of Biological Engineering


Methodology: Quantification of variation and the impact of biomass in targeted 16S rRNA gene sequencing studies – Jeffrey M. Bender – Microbiome

Aug 26, 2018

Good morning! Today’s Microbiome Digest will cover the general microbiome, skin microbiome, human gut microbiome, animal microbiome, a new technique NetoVIR for viral metagenomics, microbiome market and microbiome in the news. Enjoy reading.

General microbiome

Review: A comparative review on microbiota manipulation: lessons from fish, plants, livestock and human research – Sylvia Brugman – Frontiers in Nutrition

Skin microbiome

Antibacterial soap use impacts skin microbial communities in rural Madagascar – James J. Yu – PLOSONE

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet – Marlène Chiarello – Microbiome

Multi-site human microbiome

Identification and Visualization of a Distinct Microbiome in Ocular Surface Conjunctival Tissue – Jerome Ozkan – Immunology and Microbiology

Human gut microbiome

Age-Related Changes in the Gut Microbiota Influence Systemic Inflammation and Stroke Outcome – Monica S. Spychala – Annals of Neurology

Animal microbiome

A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs – Genevieve M. Forster – Topics in Companion Animal Medicine

Synergetic action between the rumen microbiota and bovine health – Mohamed Zeineldin – Microbial Pathogenesis

Dietary corn bran improved the diversity of microbial communities and IL-10 production in weaned pigs – Ping Liu – Frontiers in Microbiology

Plant, root, and soil microbiome

Taxonomic and Functional Changes of Bacterial Communities in the Rhizosphere of Kimchi Cabbage After Seed Bacterization with Proteus vulgaris JBLS202 – Dipto Bhattacharyya – The Plant Pathology Journal

Water and extremophile microbiome

Preprint: Copper affects composition and functions of microbial communities in marine biofilms at environmentally relevant concentrations – Natàlia Corcoll – PeerJ


Machine learning meets genome assembly – Kleber Padovani de Souza – Briefings in Bioinformatics


NetoVIR: Modular Approach to Customize Sample Preparation Procedures for Viral Metagenomics – Nádia Conceição-Neto – The Human Virome

Microbiome in the news

Gut Feeling: The Microbiome and Mental Health

Chronic malnutrition in children: A new gut microbial signature – Institut Pasteur

Microbiome market

Human Microbiome Market Expected to Grow at a CAGR of 20.9% During 2018 to 2025

Aug 08, 2018

Good morning! Today’s Microbiome Digest highlights are the modeling of the gut microbiome, trotter horse urine metabolome, selection of appropriate metagenome taxonomic classifiers and news about the improvement of gut health. Enjoy reading.

General microbiome

Mini-Review: Conducting metagenomic studies in microbiology and clinical research – Tiphaine C. Martin – Applied Microbiology and Biotechnology

Human gut microbiome

Challenges in modeling the human gut microbiome – Parizad Babaei – Nature Biotechnology

Review: Rebuilding the Gut Microbiota Ecosystem – Antonella Gagliardi – International Journal of Environmental Research and Public Health

Soil exposure modifies the gut microbiota and supports immune tolerance in a mouse model – NooraOttman – Journal of Allergy and Clinical Immunology

Animal experiments

Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility – Kristopher D. Parker – Frontiers in Microbiology

Animal microbiome

Characterization of trotter horses urine metabolome by means of proton nuclear magnetic resonance spectroscopy – Chenglin Zhu – Metabolomics

Water and extremophile microbiome

Metagenomic analysis of geothermal water reservoir sites exploring carbohydrate-related thermozymes – GirijaKaushal – International Journal of Biological Macromolecules


Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research – Irina M. Velsko – mSystems

Microbes in the news

New Emerging Research Suggests Montmorency Tart Cherries May Help Enhance Gut Health

Cherries improve gut health

July 02, 2018

Good morning! Today’s Microbiome Digest will cover the general microbiome, HIV infection and multi-site bacterial microbiota, crucial role of lung microbiome in asthma, gut microbiome in type 1 diabetes, Link between diet and metabolic syndrome, Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes, HmmUFOtu: a tool for taxonomic assignment and OTU picking and a news on plastic eating bacteria …

Events and jobs

Post-Doctoral Research Position, Oregon State University, with Dr. Stephen Giovannoni

Postdoctoral Researcher Position Characterizing Microbial Candidate Phlya at Stanford University

General microbiome

Issue: The microbiome: more than a gut reaction – John R. Wingard – Blood

Evaluation at scale of microbiome-derived metabolites as biomarker of flavan-3-ol intake in epidemiological studies – Javier I. Ottaviani – Scientific Reports

All disease begins in the gut: Influence of gastrointestinal disorders and surgery on oral drug performance – Grace B. Hatton – International Journal of Pharmaceutics

Designing microbial consortia with defined social interactions – Wentao Kong – Nature Chemical Biology

Multi-site human microbiome

HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa – Heidi Tuominen – Scientific Reports

Human respiratory microbiome

State of the Art: Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human vaginal microbiome

Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth – Aline C. Freitas – Microbiome

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes Metab Res Rev

Review: Altered Gut Microbiota: A Link Between Diet and the Metabolic Syndrome – Velasquez Manuel T – Metabolic Syndrome and Related Disorders

Chapter: Microbiota, Obesity and NAFLD – Louis H. S. Lau – Obesity, Fatty Liver and Liver Cancer

Chapter: The Influence of Gut Microbial Metabolism on the Development and Progression of Non-alcoholic Fatty Liver Disease – Wei Jia – Obesity, Fatty Liver and Liver Cancer

Method: Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Ancient Thali Diet: Gut Microbiota, Immunity, and Health – Kaitlyn Shondelmyer – Yale Journal of Biology & Medicine

Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet – Yunjian Zhang – Epilepsy Research

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut – Whitman B. Schofield – Cell Host & Microbe

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Review: The Gut Microbiome Alterations and Inflammation-Driven Pathogenesis of Alzheimer’s Disease—a Critical Review – Marta Sochocka – Molecular Neurobiology

The controversial role of Enterococcus faecalis in colorectal cancer – Carolina Vieira de Almeida – Therapeutic Advances in Gastroenterology

Animal experiments

Pea-protein alginate encapsulation adversely effects development of clinical signs of Citrobacter rodentium-induced colitis in mice treated with probiotics – Natallia Varankovich – Canadian Journal of Microbiology

Maternal Soluble Fiber Diet during Pregnancy Changes the Intestinal Microbiota, Improves Growth Performance, and Reduces Intestinal Permeability in Piglets – Chuanshang Cheng – Applied and Environmental Microbiology

Overlapping community composition of gut and fecal microbiomes in lab-reared and field-collected German cockroaches – Madhavi L. Kakumanu – Applied and Environmental Microbiology

TRIF deficiency protects non-obese diabetic mice from type 1 diabetes by modulating the gut microbiota and dendritic cells – Elke Gülden – Journal of Autoimmunity

Mucosal homeostasis is altered in the ileum of gnotobiotic mice – Chasen J. Greig – Journal of Surgical Research

Animal microbiome

Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire – Jan F. Gogarten – The ISME Journal

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes – Pablo Tsukayama – mSystems

Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian – Sarah M. Griffiths – The ISME Journal

Plant, root, and soil microbiome

Review: Multifaceted Impacts of Bacteriophages in the Plant Microbiome – Britt Koskella – Annual Review of Phytopathology

‘Concord’ grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes – R.W.Lewis – Plant Physiology and Biochemistry

Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil – Mobolaji F. Adegboye – Genome Announcements

Differences in microbial key players in anaerobic degradation between biogas and sewage treatment plants – Christian Buettner – International Biodeterioration & Biodegradation

Water and extremophile microbiome

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico – Leila J. Hamdan – Scientific Reports

Stoichio-Metagenomics of ocean waters: a molecular evolution approach to trace the dynamics of nitrogen conservation in natural communities – Hannes Dittberner – Frontiers in Microbiology

 Probiotics / prebiotics

Review: Impact of Prebiotics on Poultry Production and Food Safety – Steven C. Ricke – Yale Journal of Biology & Medicine

Isolation and Partial Characterization of Lactic Acid Bacteria from the Gut Microbiota of Marine Fishes for Potential Application as Probiotics in Aquaculture – Sergio Alonso – Probiotics and Antimicrobial Proteins

Effects of Prebiotics vs a Diet Low in Fodmaps in Patients with Functional Gut Disorder – Jose-Walter Huaman – Gastroenterology


HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies – Qi Zheng – Genome Biology


Review: Culturing the human microbiota and culturomics – Jean-Christophe Lagier – Nature Reviews Microbiology

Microbes in the news

Plastic-eating bacteria discovered by student could help solve global pollution crisis

Sewage microbes make a fuel booster

Our intestinal microbiome influences metabolism — through the immune system


Ashok’s non-microbiology picks

Efficacy and Safety of Dupilumab in Glucocorticoid-Dependent Severe Asthma – Klaus F. Rabe – The NEW ENGLAND JOURNAL of Medicine