December 1, 2018

Today’s microbiome digest will have more on gut microbiome, animal experiments along with one method DiTaxa for host phenotype and biomarker detection. Enjoy reading.

 General microbiome

Pre-transplant recovery of microbiome diversity without recovery of the original microbiome – Armin Rashidi – Bone Marrow Transplantation

Review: Importance of gut microbiota in obesity – Isabel Cornejo-Pareja – European Journal of Clinical Nutrition

Gut Microbiome and Plasma Microbiome-Related Metabolites in Patients With Decompensated and Compensated Heart Failure – Tomohiro Hayashi – Circulation Journal

Review: The lung and gut microbiome: what has to be taken into consideration for cystic fibrosis? – Geneviève Héry-Arnaud – Journal of Cystic Fibrosis

Gut microbiome

Impacts of dietary silver nanoparticles and probiotic administration on the microbiota of an in-vitro gut model – Cristina Cattò – Environmental Pollution

The Gut Microbiome: A Difficult Target for Translational Studies of Clostridium Difficile Colonization – Richard Kellermayer – Journal of Pediatric Gastroenterology and Nutrition

Altered gut microbiota after traumatic splenectomy is associated with endotoxemia – Hua Zhu – Emerging Microbes & Infections

Gut Microbiota Modulates Interactions Between Polychlorinated Biphenyls and Bile Acid Homeostasis – Sunny Lihua Cheng – Toxicological Sciences

The intestinal microbiome and its relevance for functionality in older persons – Andrea Ticinesi – Current Opinion in Clinical Nutrition and Metabolic Care

Gut Microbiota Disruption in Septic Shock Patients: A Pilot Study – You-Dong Wan – Medical Science Monitor

Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants – Bing Ma – Frontiers in Microbiology

Review: Microbial impact on cholesterol and bile acid metabolism: current status and future prospects – Aicha Kriaa – Journal of Lipid Research

Respiratory microbiome

Characterising the respiratory microbiome – Rebecca L. Watson – European Respiratory Journal

Vaginal microbiome

Characterization of vaginal microbiota in Thai women – Auttawit Sirichoat – PeerJ

Normal vaginal microbiome in women with primary Sjögren’s syndrome-associated vaginal dryness – van der Meulen TA – Annals of the Rheumatic Diseases

Animal experiments

On the role of corticosterone in behavioral disorders, microbiota composition alteration and neuroimmune response in adult male mice subjected to maternal separation stress – HosseinAmini-Khoei – International Immunopharmacology

Insights into a Possible Mechanism Underlying the Connection of Carbendazim-Induced Lipid Metabolism Disorder and Gut Microbiota Dysbiosis in Mice – Cuiyuan Jin – Toxicological Sciences

General Anesthesia Alters the Diversity and Composition of the Intestinal Microbiota in Mice – Mara A. Serbanescu – Anesthesia & Analgesia

Lactobacillus helveticus KLDS1.8701 alleviates D-galactose-induced aging by regulating Nrf-2 and gut microbiota in mice – Bailiang Li – Food and Function

The Host Microbiota Contributes to Early Protection Against Lung Colonization by Mycobacterium tuberculosisAlexia Dumas – Frontiers in Immunology

Cesarean Section Induces Microbiota-Regulated Immune Disturbances in C57BL/6 Mice – Line Fisker Zachariassen – The Journal of Immunology


DiTaxa: Nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection – Ehsaneddin Asgari – Bioinformatics


November 24, 2018

In today’s microbiome digest there are various papers on human, animal and plant microbiome specifically the microbiome of coral, Honey Bee, Welsh Mountain ponies, root and rhizosphere. Enjoy reading.

Events and jobs

Senior Bioinformatics Scientist, Microbiome

General microbiome

Essay: Microbiome dynamics in obesity – Christoph A. Thaiss – Science

Human microbiome diversity: implications in health, disease, and applications – Kathryn J. Pflughoeft – Annual Reviews

Gut microbiome

Review: Gut microbiota and aging – Francesca Mangiola – European Review for Medical and Pharmacological Sciences

Review: Microbial community reshaped in gastric cancer – L.-L. Wang – European Review for Medical and Pharmacological Sciences

Differential clustering of faecal and mucosa‐associated microbiota in healthy individuals – Adam Carstens – Journal of Digestive Diseases

The prevalence and transcriptional activity of the mucosal microbiota of ulcerative colitis patients – Aina E. Fossum Moen – Scientific Reports

Skin microbiome

The Influence of Habitat and Phylogeny on the Skin Microbiome of Amphibians in Guatemala and Mexico – Silas Ellison – Microbial Ecology

Respiratory microbiome

Inhaled nanomaterials and the respiratory microbiome: clinical, immunological and toxicological perspectives – Tuang Yeow Poh – Particle and Fibre Toxicology

Animal experiments

An intermittent hypercaloric diet alters gut microbiota, prefrontal cortical gene expression and social behaviours in rats – Reichelt AC – Nutritional Neuroscience

Animal microbiome

Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny – F. Joseph Pollock – Nature Communications

Gut and Whole-Body Microbiota of the Honey Bee Separate Thriving and Non-thriving Hives – Céline Ribière – Microbial Ecology

Gut microbiome composition is associated with spatial structuring and social interactions in semi-feral Welsh Mountain ponies – Rachael E. Antwis – Microbiome

Plant, root, and soil microbiome

The structure and function of the global citrus rhizosphere microbiome – Jin Xu – Nature Communications

Root microbiome response to treated wastewater irrigation – AvihaiZolti – Science of The Total Environment

Water and extremophile microbiome

New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures – Ying Liu – Environmental Microbiology

Probiotics / prebiotics

Review: Probiotics, prebiotics and synbiotics for weight loss and metabolic syndrome in the microbiome era – R. Ferrarese – European Review for Medical and Pharmacological Sciences

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