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.

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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

Do your eyes have microbiomes? How does heavy rain influence the Atacama desert microbiome?  Welcome to the microbiome digest. This weekends articles also include the latest research on space-station microbes, the influence of protists on the rhizosphere, techniques in metabolome/microbiome research and more! Enjoy!

General microbiome

Identifying and Predicting Novelty in Microbiome Studies – Xiaoquan Su – mBio

Pregnancy and early life

Impacts of diet and exercise on maternal gut microbiota are transferred to offspring – Shyam Prakaash Bhagavata Srinivasan – Frontiers in Endocrinology

Multi-site human microbiome

Biogeography of the human ocular microbiota – JeromeOzkan – The Ocular Surface

Review: The Human Microbiota and Asthma – Aaron Ver Heul – Clinical Reviews in Allergy & Immunology

Human gut microbiome

Gastroduodenal “Dysbiosis”: a New Clinical Entity – Ayesha Shah – Current Treatment Options in Gastroenterology

Animal experiments

Preprint: Colonization of the tsetse fly midgut with commensal Enterobacter inhibits trypanosome infection establishment – Brian L Weiss – bioRiv

Animal microbiome

Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation – Hooman Derakhshani – Microbiome

Plant, root, and soil microbiome

Protists: Puppet Masters of the Rhizosphere Microbiome – ZhileiGao – Trends in Plant Science

Characterization of microbes and denitrifiers attached to two species of floating plants in the wetlands of Lake Taihu – Bing Han – PLOS ONE

Environmental and spatial variables determine the taxonomic but not functional structure patterns of microbial communities in alpine grasslands – Xiao-BoWang – Science of The Total Environment

With or without trees: Resistance and resilience of soil microbial communities to drought and heat stress in a Mediterranean agroforestry system – EstherGuillot – Soil Biology and Biochemistry

Response of microbial communities and enzyme activities to amendments in saline-alkaline soils – ShaohuaShi – Applied Soil Ecology

The effect of moisture on soil microbial properties and nitrogen cyclers in Mediterranean sweet orange orchards under organic and inorganic fertilization – AliciaMorugán-Coronado – Science of The Total Environment

Water and extremophile microbiome

Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces – Nitin Kumar Singh – Microbiome

Unprecedented rains decimate surface microbial communities in the hyperarid core of the Atacama Desert – A. Azua-Bustos – Scientific Reports

Exposure to tetracycline perturbs the microbiome of soil oligochaete Enchytraeus crypticus – JunMa – Science of The Total Environment

Preprint: Filamentation of Vibrio cholerae is an adaptation for surface attachment and biofilm architecture – Benjamin R Wucher – bioRxiv

Designing an in situ remediation strategy for polluted surface water bodies through the specific regulation of microbial community – Boran Wu – Frontiers of Environmental Science & Engineering

Food microbiology

Microbiome of drinking water: A full-scale spatio-temporal study to monitor water quality in the Paris distribution system – YoannPerrin – Water Research

Techniques

Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications – Edward E. K. Baidoo – Microbial Metabolomics

High-Throughput Solid-Phase Microextraction–Liquid Chromatography–Mass Spectrometry for Microbial Untargeted Metabolomics – Fatemeh Mousavi – Microbial Metabolomics

Papers on metabolism, cancer and dietary fiber in this digest!

General Microbiome

Translating microbiome futures – Taroncher-Oldenburg G et al. – Nature Biotechnology

Human gut Microbiome

Prolonged Antibiotic Treatment Generates a Fluoroquinolone Resistant Gut Microbiome and Collateral Multi-Drug Resistance – Dubinsky et al. – biorxiv

Shifts in microbial transcription patterns prior to onset of Necrotizing enterocolitis may indicate low oxygen levels in the gut – Sher et al. – biorxiv

Dietary metabolism, the gut microbiome, and heart failure. – Tang WHW – Nature Reviews Cardiology

Long term but not short term exposure to obesity related microbiota promotes host insulin resistance. – Foley KP – Nature Communications 

Stability of vitamin B12 with the protection of whey proteins and their effects on the gut microbiome. – Wang H – Food Chemistry

Tongue Coating Microbiota Community and Risk Effect on Gastric Cancer. – Wu J – Cancer

Human Pregnancy Microbiome

Perinatal antibiotic exposure alters composition of murine gut microbiota and may influence later responses to peanut antigen. – Boutin RCT – Allergy Asthma Clin Immunol.

Animal experiments 

Effects of dietary fiber supplementation on fatty acid metabolism and intestinal microbiota diversity in C57BL/6J mice fed with high fat diet. – Zhai X et al – Journal of Agricultural Food Chemistry

Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis. – Ma C – Microbiome

Plant, root, and soil Microbiome

Comparing DNA, RNA and protein levels for measuring microbial activity in nitrogen-amended soils  Orellana et al. – biorxiv

Water and Extremophile Microbiome

Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean. – Enav H et al. – Nature Communications

Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment. – Lang XL – Archaea

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Bioinformatics

GutLogo: Agent-based modeling framework to investigate spatial and temporal dynamics in the gut microbiome. Lin C et al. – PLoS One

Swathi’s non-microbiology picks

Building a local community of practice in scientific programming for Life Scientists – Sarah L. R. Stevens – biorxiv

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 T_H17 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

Techniques

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

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