June 11, 2019

Today’s digest is about microbiome and Alzheimer’s disease association, global survey of arsenic related genes in soil microbiome,  Bifidobacterium bifidus in infant gut and a preprint on selection in host microbiome evolution.

General microbiome

Understanding the Role of the Gut Microbiome and Microbial Metabolites in Obesity and Obesity-Associated Metabolic Disorders: Current Evidence and Perspectives – Natalia Vallianou – Current Obesity Reports

Alzheimer’s disease and symbiotic microbiota: an evolutionary medicine perspective – Molly Fox – Annals of the New York Academy of Sciences

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis – Jessica L. Mark Welch – Annual Review of Microbiology

Human microbiome

Colonic mucosal and exfoliome transcriptomic profiling and fecal microbiome response to a flaxseed lignan extract intervention in humans – Johanna W. Lampe – American journal of Clinical Nutrition

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals – Riccardo Vasapolli – Gastroenterology

Identification of Salivary Microbiota and its Association with Host Inflammatory Mediators in Periodontitis – Anna Lundmark – Frontiers in Cellular and Infection Microbiology

Effect of the Degree of Polymerization of Fructans on Ex Vivo Fermented Human Gut Microbiome – Erola Astó – Nutrients

Inflammatory skin is associated with changes in the skin microbiota composition on the back of severe acne patients – Marie-Ange Dagnelie – Experimental Dermatology

Gut microbiota development of preterm infants hospitalised in intensive care units – H. Tauchi – Beneficial Microbes

Animal experiments

Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota – Devin B. Holman – Microbiome

Sequential changes in the host gut microbiota during infection with the intestinal parasitic nematode Strongyloides venezuelensis – Tanzila Afrin – Frontiers in Cellular and Infection Microbiology

Plant, root, soil microbiome

A global survey of arsenic-related genes in soil microbiomes – Taylor K. Dunivin – BMC Biology

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics – Nengfei Wang – Microbes and Environments

Water microbiome and extremophiles

Comparison of the microbiomes of two drinking water distribution systems—with and without residual chloramine disinfection – Michael B. Waak – Microbiome

Probiotics

Probiotics may not prevent the deterioration of necrotizing enterocolitis from stage I to II/III – Zheng-Li Wang – BMC Pediatrics

Bifidobacterium bifidum and the infant gut microbiota: an intriguing case of microbe‐host co‐evolution – Sabrina Duranti – Environmental Microbiology

Techniques

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes – G.A.Arango-Argoty – Microbiome

Metabolic route computation in organism communities – Markus Krummenacker – Microbiome

The role of multilevel selection in host microbiome evolution – Simon van Vliet – BioRxiv

Microbes and the market

Human Microbiome Therapeutics Market Analysis 2019: With Top 20 Countries data, Product Types, Segmentation, Market Share Analysis, Influential Trends And Challenges, Forecast To 2023 – Saginaw Daily

Global Human Microbiome Based Drugs and Diagnostics Market Potential Growth 2019 | Second Genome Inc., Enterome Bioscience, Yakult – Business Tech Hub

Human Microbiome Market 2024 Significant Development | Future Trends of Key Players by Size and Share – The Warren Daily

In-Depth Research Report of Global Microbiome Sequencing Services Market (2019 Version), with Types, Application, and Manufactures – the Pueblo Daily

Microbiome Sequencing Services Market Key Players, Industry Overview, Demand & Supply Chain Analysis, Forecast To 2024 – Burbank Observer

Human Microbiome Market Growth, Trend and Forecast 2018-2026 – Business Herald

 

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May 4, 2019

Have a good weekend! Today, in this MB, we have interesting papers about different aspects of the microbiome. For example, we have a review overviewing the relationship between epigenetic changes, microbiome and metabolic diseases, as well as a paper focused in the use of a microbial metabolite in the prognosis of coronary issues. We have also the publication of an interesting study authored by the MB founder Elisabeth Bik.

There are also some papers about coral microbiome and an study about the homogenization of the microbiome between both US Air Force cadets and their built environment.

 

Human and General Microbiome

Review: Epigenetic Markers and Microbiota/Metabolite-Induced Epigenetic Modifications in the Pathogenesis of Obesity, Metabolic Syndrome, Type 2 Diabetes, and Non-alcoholic Fatty Liver Disease – Daniela Stols-Gonçalves – Current Diabetes Reports

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth Bik – PLoS ONE

Trimethyllysine, a trimethylamine N-oxide precursor, provides near- and long-term prognostic value in patients presenting with acute coronary syndromes – Xinmin S Li – European Heart Journal

Review: The interaction between Entamoeba histolytica and enterobacteria shed light on an ancient antibacterial response – Nancy Guillén – Cellular Microbiology

PCR Characterization of Microbiota on Contracted and Non-Contracted Breast Capsules – Yara Bachour – Aesthetic Plastic Surgery

Decreased Cephalosporin Susceptibility of Oropharyngeal Neisseria Species in Antibiotic-Using Men-who-have-sex-with-men of Hanoi, Vietnam– Huan V Dong – Clinical Infectious Diseases

Review: Smoking and periodontal microorganisms – Takashi Hanioka – Japanese Dental Science Review

The influence of the vaginal microbiota on preterm birth: A systematic review and recommendations for a minimum dataset for future research – Myrthe JCS. Peelen – Placenta

Gut Microbiome in Health and Disease: Emerging Diagnostic Opportunities – Aonghus Lavelle – Gastroenterology Clinics of North America

Laryngotracheal Microbiota in Adult Laryngotracheal Stenosis – Alexander T. Hillel – mSphere

Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes – Pedro Escudeiro –  mSphere

 

Beneficial Microbes

Review: Changing our microbiome: Probiotics in dermatology – Y. Yu – British Journal of Dermatology

Amelioration of obesity-related biomarkers by Lactobacillus sakei CJLS03 in a high-fat diet-induced obese murine model – Josep Ji – Scientific Reports

 

Animal Models / Animal Microbiome

Age-related analysis of the gut microbiome in a purebred dog colony – Keijiro Mizukami – FEMS Microbiology Letters

Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus) – Christina F. Butowski – PLoS ONE

Effects of diet on gut microbiota of soil collembolans – Qian Xiang – Science of The Total Environment

Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome – Rebecca L. Maher – Scientific Reports

Structure and stability of the coral microbiome in space and time – Courtney M. Dunphy – Scientific Reports

The effect of dissolved nickel and copper on the adult coral Acropora muricata and its microbiome – Francesca Gissi – Environmental Pollution

 

Food Microbiome

Microbiota and Chemical Compounds in Fermented Pinelliae Rhizoma (Banxiaqu) from Different Areas in the Sichuan Province, China – Bo Shu – Polish Journal of Microbiology

 

Built Environment

Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets –  Anukriti Sharma – Microbiome

 

Environmental Microbiome

The Influence of Temperature and Nitrogen Source on Cellulolytic Potential of Microbiota Isolated from Natural Environment –  Agnieszka Wita  – Polish Journal of Microbiology

 

Techniques

The potential of nanoflow liquid chromatography-nano electrospray ionisation-mass spectrometry for global profiling the faecal metabolome – Andrew J. Chetwynd – Journal of Chromatography A

April 28, 2019

Human Gut and General Microbiome

Review: Stereotypes About Enterotype: the Old and New Ideas – Mingyue Cheng – Genomics, Proteomics & Bioinformatics

Review: Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity – Eric M. Brown –  Annual Review of Immunology

Review: The Microbiome and Food Allergy – Onyinye I. Iweala – Annual Review of Immunology

Review: An Updated Review of Clostridium difficile Treatment in Pediatrics – Christopher T. Campbel –  The Journal of Pediatric Pharmacology and Therapeutics

Review: Pediatric inflammatory bowel disease: continuous lessons for adult inflammatory bowel disease – Shahzad Ahmed – Current Opinion in Gastroenterology

Review: Intestinal Microbiota in Cardiovascular Health and Disease: JACC State-of-the-Art Review – W.H. Wilson Tang – Journal of the American College of Cardiology

Review: The role of the gut microbiome in sex differences in arterial pressure – Anna L. Beale – Biology of Sex Differences

Review: Precision Nutrition and the Microbiome, Part I: Current State of the Science – Susan Mills – Nutrients

Review: Impact of bariatric surgery on type 2 diabetes: contribution of inflammation and gut microbiome? – Jean Debédat – Seminars in Immunopathology

Review: The Gut Microbiota-Host Partnership as a Potential Driver of Kawasaki Syndrome – Susanna Esposito – Frontiers in Pediatrics

Review: A Review of Mixed Strain Clostridium difficile Colonization and Infection – Pete Dayananda – Frontiers in Microbiology

Review: Small Intestinal Bacterial Overgrowth in Patients With Cirrhosis – Gaurav Ghosh – Journal of Clinical and Experimental Hepatology

Perspective: Effect of Metformin on Antipsychotic-Induced Metabolic Dysfunction: The Potential Role of Gut-Brain Axis – Chao Luo –  Frontiers in Pharmacology

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome – Jun Li – Genomics, Proteomics & Bioinformatics

Contribution of Non-immune Cells to Activation and Modulation of the Intestinal Inflammation – Renata Curciarello – Frontiers in Immunology

Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan – Yukuto Sato – Scientific Reports

The short-chain fatty acid propionate increases glucagon and FABP4 production, impairing insulin action in mice and humans – Amir Tirosh – Science Translational Medicine

 

Cancer and Microbiome

The diversity of gut microbiome is associated with favorable responses to anti-PD-1 immunotherapy in Chinese non-small cell lung cancer patients – Yueping Jin – Journal of Thoracic Oncology

Gut Microbiota as a Positive Potential Therapeutic Factor in Carcinogenesis: an Overview of Microbiota-Targeted Therapy – Farahnaz Joukar – Journal of Gastrointestinal Cancer

Detection of Fusobacterium nucleatum in stool and colonic tissues from Norwegian colorectal cancer patients – Hege Smith Tunsjø – European Journal of Clinical Microbiology & Infectious Diseases

 

Oral Microbiome

Gender-Specific Associations Between Saliva Microbiota and Body Size  – Sajan C. Raju – Frontiers in Microbiology

Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis – Bo-Young Hong – Microbiome

 

Respiratory Tract Microbiome

The airway microbiota in children newly diagnosed with bronchiectasis largely retains its diversity – Naveen Pillarisetti – European Respiratory Journal

Performance of the Biomark HD real-time qPCR System (Fluidigm) for the detection of nasopharyngeal bacterial pathogens and Streptococcus pneumoniae typing – Courtney P. Olwagen – Scientific Reports

 

Mother and Child Microbiome

Systematic Review: Repertoire of human breast and milk microbiota: a systematic review – Amadou Togo – Future Medicine

Variation of cultured skin microbiota in mothers and their infants during the first year postpartum – Georgios Gaitanis – Pediatric Dermatology

 

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment – Ning Li – Genomics, Proteomics & Bioinformatics

 

Reproductive tract Microbiome

Impact of reproductive aging on the vaginal microbiome and soluble immune mediators in women living with and at-risk for HIV infection – Kerry Murphy – PLoS ONE

The Vaginal and Urinary Microbiomes in Premenopausal Women With Interstitial Cystitis/Bladder Pain Syndrome as Compared to Unaffected Controls: A Pilot Cross-Sectional Study – Kate V. Meriwether – Frontiers in Cellular and Infection Microbiology

Microorganisms in the healthy upper reproductive tract: from denial to beneficial assignments for reproductive biology – Rebekka Einenkel – Reproductive Biology

 

Animal Microbiome

Structural shifts in the intestinal microbiota of rats treated with cyclosporine A after orthotropic liver transplantation – Junjun Jia – Frontiers of Medicine

Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax) – Wen Wang – International Microbiology

Antibiotics-induced perturbations in gut microbial diversity influence metabolic phenotypes in a murine model of high-fat diet-induced obesity – Dongmin Liu – Applied Microbiology and Biotechnology

Rumen fermentation, intramuscular fat fatty acid profiles and related rumen bacterial populations of Holstein bulls fed diets with different energy levels – Haibo Wang – Applied Microbiology and Biotechnology

The Gut Microbiome on a Periodized Low-Protein Diet Is Associated With Improved Metabolic Health – Zhencheng Li – Frontiers in Microbiology

Human activity can influence the gut microbiota of Darwin’s finches in the Galapagos Islands – Sarah A. Knutie – Molecular Ecology

Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters – Colin Fogarty – Journal of Applied Microbiology

Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea – Haiyan Xu – Food & Nutrition

Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut – Rafal Tokarz – Ticks and Tick-borne Diseases

Human gut microbiota transferred to germ-free NOD mice modulate the progression towards type 1 diabetes regardless of the pace of beta cell function loss in the donor – Vit Neuman – Diabetologia

Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors – Barbora Pafčo – American Journal of Physical Anthropology

The bumble bee microbiome increases survival of bees exposed to selenate toxicity – Jason A. Rothman – Environmental Microbiology

Effect of probiotic supplementation on seizure activity and cognitive performance in PTZ-induced chemical kindling – Samaneh Bagheri – Epilepsy and Behavior

Inulin Can Alleviate Metabolism Disorders in ob/ob Mice by Partially Restoring Leptin-Related Pathways Mediated by Gut Microbiota – Xiaofeng Song – Genomics, Proteomics & Bioinformatics

Supplementation with compound polysaccharides contributes to the development and metabolic activity of young rat intestinal microbiota – Mengxia Wang – Food & Nutrition

A Risky Business? Habitat and Social Behavior Impact Skin and Gut Microbiomes in Caribbean Cleaning Gobies – Raquel Xavier – Frontiers in Microbiology

Ovarian progesterone suppresses depression and anxiety-like behaviors by increasing the Lactobacillus population of gut microbiota in ovariectomized mice – Watcharin N.Sovijit – Neuroscience Research

 

Beneficial Microbes and Compounds

Meta-analysis: Probiotics improve glucose and lipid metabolism in pregnant women: a meta-analysis – Man-Man Han – Annals of Translational Medicine

Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis – Jiachao Zhang – mSystem

Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts – Guangwen Luo – Frontiers in Microbiology

The beneficial effects of purple yam (Dioscorea alata L.) resistant starch on hyperlipidemia in high-fat-fed hamsters – Tao Li – Food & Nutrition

Restoration of Bacterial Microbiome Composition and Diversity Among Treatment Responders in a Phase 2 Trial of RBX2660: An Investigational Microbiome Restoration Therapeutic – Ken F Blount – Open Forum Infectious Diseases

Lactobacillus reuteri DSM 17938 – A comparative study on the effect of probiotics and lysates on human skin – I. Khmaladze – Experimental Dermatology

 

Plant and Soil Microbiome

Nodulation induces systemic resistance of Medicago truncatula and Pisum sativum against Erysiphe pisi and primes for powdery mildew-triggered salicylic acid accumulation – Lara Smigielski – IS-MPMI

Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest – Gileno V. Lacerda-Júnior – Frontiers in Microbiology

Microbial Diversity in the Edible Gall on White Bamboo Formed by the Interaction between Ustilago esculenta and Zizania latifolia – Zhihao Tu – Current Microbiology

Species-specific response of the soil collembolan gut microbiome and resistome to soil oxytetracycline pollution – Qi Zhang – Science of The Total Environment

 

Food Microbiome

Gamma Irradiation Influences the Survival and Regrowth of Antibiotic-Resistant Bacteria and Antibiotic-Resistance Genes on Romaine Lettuce – Vaishali Dharmarha – Frontiers in Microbiology

 

Bioinformatics

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes – Xiaoqing Jiang – Genomics, Proteomics & Bioinformatics

Phy-PMRFI: Phylogeny-aware Prediction of Metagenomic Functions using Random Forest Feature Importance – Jyotsna Talreja Wassan – IEEE Transactions on NanoBioscience

 

Other

Flood Season Microbiota from the Amazon Basin Lakes: Analysis with Metagenome Sequencing – Célio Dias Santos Júnior – Microbiology Resource Announcements

Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium – Mathew P. Watts – Water Research

April 1, 2019

In today’s digest read about covert pathogenesis in urinary tract, microbial fuel cells in treatment of organic acid fermentation wastewater, gut microbial metabolism in weanling pigs, and more. Enjoy!

Urinary microbiome

*Covert pathogenesis: Transient exposures to microbes as triggers of disease – Nicole M. Gilbert, Amanda L. Lewis – PlosPathogens

Evaluation of antibacterial efficacy of sulfur nanoparticles alone and in combination with antibiotics against multidrug-resistant uropathogenic bacteria – Priti Paralikar – Journal of Environmental Science and Health, Part A

Review: A Comprehensive Review of Overactive Bladder Pathophysiology: On the Way to Tailored Treatment – Benoit Peyronnet – European Urology

Vaginal microbiome

Effect of progesterone on Candida albicans biofilm formation under acidic conditions: a transcriptomic analysis – Bruna Gonçalves – bioRxiv

Skin microbiome

Cutibacterium acnes antibiotic production shapes niche competition in the human skin microbiome – Jan Claesen – bioRxiv

Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome – Xinzhao Tong – mSystems

Gut Microbiome

The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding – Yu Liu – Frontiers in Microbiology

Gut Microbiome Functional and Taxonomic Diversity within an Amazonian semi-nomadic hunter-gatherer group – Liliane Costa Conteville – bioRxiv

Risk of inflammatory bowel disease after Campylobacter jejuni and Campylobacter concisus infection: a population-based cohort study – Hans Mittle Nielsen – Scandinavian Journal of Gastroenterology

Unilateral ureteral obstruction causes gut microbial dysbiosis and metabolome disorders contributing to tubulointerstitial fibrosis – Lin Chen – Experimental & Molecular Medicine

Oral microbiome

Polymicrobial synergy within oral biofilm promotes invasion of dendritic cells and survival of consortia members – Ahmed El-Awady – Biofilms and Microbiomes

Animal microbiome

*Metagenomic reconstructions of gut microbial metabolism in weanling pigs – Weilan Wang – Microbiome

Probiotics/Prebiotics

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling – Juliana M. Ansari – PlosOne

Biosurfactant Production by Lactic Acid Bacterium Pediococcus dextrinicus SHU1593 Grown on Different Carbon Sources: Strain Screening Followed by Product Characterization – Abouzar Ghasemi – Scientific Reports

Phages and viruses

Bacteriophage adherence to mucus mediates preventive protection against pathogenic bacteria – Gabriel MF Almeida – bioRxiv

Review: The gut virome: the ‘missing link’ between gut bacteria and host immunity? – Indrani Mukhopadhya – Therapeutic Advances in Gastroenterology

Soil microbiome

Shift of the microbial communities from exposed sandstone rocks to forest soils during pedogenesis – Yaping Liu – International Biodeterioration & Biodegradation

Water and extremophile microbiome

Startup, performance, and microbial communities of an anammox reactor inoculated with indigenous sludge for the treatment of high-salinity and mesophilic underground brine – Nobuyuki Yokota – Clean Technologies and Environmental Policy

*Power generation and microbial community analysis in microbial fuel cells: A promising system to treat organic acid fermentation wastewater – Tian Xia – Bioresource Technology

Techniques

Cultivating in situ triggers growth of previously uncultivated microorganisms via a growth initiation factor in nature – Dawoon Jung – bioRxiv

Bioinformatics

Library preparation and sequencing platform introduce bias in metagenomics characterisation of microbial communities – Casper S. Poulse – bioRxiv

March 27, 2019

Happy Wednesday! Today’s digest includes spider endosymbionts, microbes shared between family members, and the effects of plastic on the microbiome of compost. Enjoy!

General microbiome

Transmission of human-associated microbiota along family and social networks – Brito – Nature Microbiology

Diversity-disease relationships and shared species analyses for human microbiome-associated diseases – Ma – ISME

Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity – Fodelianakis – Nature Communications

Preprint: Exploring the archaeome: detection of archaeal signatures in the human body – Pausan – bioRxiv

Human gut microbiome

Sucrose 6F-phosphate phosphorylase: a novel insight in the human gut microbiome – Tauzin – Microbial Genomics

Human skin microbiome

Preprint: Moving microbes: the dynamics of transient microbial residence on human skin – Vandegrift – bioRxiv

Animal experiments

Effects of phycocyanin in modulating the intestinal microbiota of mice – Xie – MicrobiologyOpen

Animal microbiome

Preprint: Endosymbiotic bacteria are prevalent and diverse in agricultural spiders – White – bioRxiv

Plant, root, and soil microbiome

Litter Quality Modulates Effects of Dissolved Nitrogen on Leaf Decomposition by Stream Microbial Communities – Jabiol – Microbial Ecology

Additions of sugar and nitrogenous fertiliser affect plant nitrogen status and soil microbial communities – Morrow – Applied Soil Ecology

Characterizing differences in microbial community composition and function between Fusarium wilt diseased and healthy soils under watermelon cultivation – Wang – Plant and Soil

Meta-analysis shows positive effects of plant diversity on microbial biomass and respiration – Chen – Nature Communications

Effects of transgenic glufosinate-tolerant rapeseed (Brassica napus L.) and the associated herbicide application on rhizospheric bacterial communities – Tang – Physiological and Molecular Plant Pathology

Structure and Diversity of Soil Bacterial Communities in Offshore Islands – Lin – Scientific Reports

The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China – Chen – Applied Microbiology and Biotechnology

Variation in rhizosphere priming and microbial growth and carbon use efficiency caused by wheat genotypes and temperatures – Yin – Soil Biology and Biochemistry

Using a soil bacterial species balance index to estimate potato crop productivity – Jeanne – PLoS One

Limited effect of planting transgenic rice on the soil microbiome studied by continuous 13CO2 labeling combined with high-throughput sequencing – Wang – Applied Microbiology and Biotechnology

Range-expansion effects on the belowground plant microbiome – Ramirez – Nature Ecology and Evolution

Water and extremophile microbiome

Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments – Marshall – ISME

Built environment

Exploring the long-term effect of plastic on compost microbiome – Esan – PLoS One

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced “iron mound” sediments – Leitholf – PLoS One

Probiotics/prebiotics

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling – Ansari – PLoS One

Review: Importance of probiotics in the prevention and treatment of colorectal cancer – Eslami – Journal of Cellular Physiology

Techniques

Robust sampling and preservation of DNA for microbial community profiling in field experiments – Groenenboom – BMC Research Notes

March 20, 2019

Today’s digest features a longitudinal survey of maternal anti-viral antibodies in newborns that provides a blueprint for understanding infectious disease susceptibility, a detailed overview of antimicrobial resistance identification and characterization methods (from traditional antimicrobial susceptibility testing to recent deep-learning methods), and more. Happy reading!

Gut microbiome

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention – Jessica A Grembi – bioRxiv

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3 – Zheng Kuang – bioRxiv

*Neuronal programming by microbiota enables environmental regulation of intestinal motility – Yuuki Obata – bioRxiv

Probiotics

Growth Mode and Carbon Source Impact the Surfaceome Dynamics of Lactobacillus rhamnosus GG – Kirsi Savijoki – bioRxiv

Nasal microbiome

The nasal and oropharyngeal microbiomes of healthy livestock workers – Ashley E. Kates – PlosOne

Vaginal microbiome

Mini review: Vaginal microbiota transplantation for the treatment of bacterial vaginosis: a conceptual analysis – Dongwen Ma – FEMS Microbiology Letters

Comparative study of vulva and abdominal skin microbiota of healthy females with high and average BMI – Rebecca Vongsa – BMC Microbiology

Plant/root/soil microbiome

Biosurfactant production by a rhizosphere bacteria Bacillus altitudinis MS16 and its promising emulsification and antifungal activity – Madhurankhi Goswami & Suresh Deka – Colloids and Surfaces B: Biointerfaces

Microbial diversity and soil physiochemical characteristic of higher altitude – Saurabh Kumar – PlosOne

Water microbiome

Ecological processes underpinning microbial community structure during exposure to subinhibitory level of triclosan – Seungdae Oh – Scientific Reports

Microbial Ecology of Snow Reveals Taxa-Specific Biogeographical Structure – Shawn P. Brown & Ari Jumpponen – Microbial Ecology

Phages and viruses

*The repertoire of maternal anti-viral antibodies in human newborns – Christian Pou – Nature Medicine

Methods

*Review: Sequencing-based methods and resources to study antimicrobial resistance – Manish Boolchandani – Nature Reviews Genetics

March 17, 2019

Have a good sunday! Today, we have a quite long digest, containing a variety of articles and studies: reviews about the microbiome and breastfeeding and Parkinson’s disease; microbiota alterations in pulmonary fibrosis, association with stress in pregnant women, and relationships between oral microbiome and pancreatic cancer. And so much more!

 

Human/General Microbiome

Review: Microbiome programming of brain development: implications for neurodevelopmental disorders – Hans Forssberg – Developmental Medicine and Child Neurology

Review: Microbiome, Parkinson’s Disease and Molecular Mimicry – Fabiana Miraglia – Cells

Review: The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut – Janneke Elzinga – Microbiology and Molecular Biology Reviews

Review: Indoles: metabolites produced by intestinal bacteria capable of controlling liver disease manifestation – T. Hendrikx – Journal of Internal Medicine

Review: Shaping the Gut Microbiota by Breastfeeding: The Gateway to Allergy Prevention? – Lieke W. J. van den Elsen – Frontiers in Pediatrics

Minireview: Nonalcoholic fatty liver disease and the gut microbiome: Are bacteria responsible for fatty liver? – Tien S Dong – Experimental Biology and Medicine

Perspectives: Is the fountain of youth in the gut microbiome?John F. Cryan – The Journal of Physiology

Bugs to debug? The exploration of gut microbiome in human health and diseases – Yen-Hsuan Ni – Journal of the Formosan Medical Association

Impact of a bathing tradition on shared gut microbe among Japanese families – Toshitaka Odamaki – Scientific Reports

Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome – Promi Das – BMC Genomics

Fecal and blood microbiota profiles and presence of nonalcoholic fatty liver disease in obese versus lean subjects – Yeojun Yun – PLoS One

H. pylori eradication with antibiotic treatment causes changes in glucose homeostasis related to modifications in the gut microbiota – Gracia Mª Martín-Núñez – PLoS One

Oral microbial dysbiosis in patients with Kostmann syndrome – Nursen Topcuoglu – Journal of Medical Microbiology

Alterations in the gut microbiota of patients with silica-induced pulmonary fibrosis – Yao Zhou – Journal of Occupational Medicine and Toxicology

Association between Psychosocial Stress and Fecal Microbiota in Pregnant Women – C. Hechler – Scientific Reports

Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients – Fu‑Gang Wang – Experimental and Therapeutic Medicine

Role of Fecal Microbiota Transplantation for Maintenance of Remission in Patients with Ulcerative Colitis: A Pilot Study – Ajit Sood – Journal of Crohn’s and Colitis

Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women – Liying Yang – Emerging Microbes & Infections

Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans – Anna M. Seekatz – mSphere

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression – Florian R. Kirchner – Frontiers in Immunology

Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer – Rogier Aäron Gaiser – Gut

Disordered intestinal microbes are associated with the activity of Systemic Lupus Erythematosus – Yao Li – Clinical Science

Long-Term Azithromycin Reduces Haemophilus influenzae and Increases Antibiotic Resistance in Severe Asthma – Steven L Taylor – American Journal of Respiratory and Critical Care Medicine

Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon – Shawn Gurwara – Nutrients

Analysis of the Effects of Dietary Pattern on the Oral Microbiome of Elite Endurance Athletes – Nida Murtaza – Nutrients

 

Animal Microbiome / Animal Experiments

TLR4 May Be Involved in the Regulation of Colonic Mucosal Microbiota by Vitamin A – Lu Xiao – Frontiers in Microbiology

Tunicate-associated bacteria show a great potential for the discovery of antimicrobial compounds – Diah Ayuningrum – PLoS One

Effects of Arsenic on Gut Microbiota and Its Biotransformation Genes in Earthworm Metaphire sieboldi – Hong-Tao Wang – Environmental Science and Technology

A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract – Saad Al-Masaudi – International Microbiology

Species identity dominates over environment in shaping the microbiota of small mammals – S. C. L. Knowles – Ecology Letters

Three types of gut bacteria collaborating to improve Kui Jie’an enema treat DSS-induced colitis in mice – Wei Yu – Biomedicine & Pharmacotherapy

The Skin Commensal Yeast Malassezia Triggers a Type 17 Response that Coordinates Anti-fungal Immunity and Exacerbates Skin Inflammation – Florian Sparber – Cell Host Microbe

Dietary inulin alleviates diverse stages of type 2 diabetes mellitus via anti-inflammation and modulating gut microbiota in db/db mice – Ke Li – Food & Function

Apple consumption is associated with a distinctive microbiota, proteomics and metabolomics profile in the gut of Dawley Sprague rats fed a high-fat diet – Jose F. Garcia-Mazcorro – PLoS One

Sema3A – mediated modulation of NR1D1 expression may be involved in the regulation of axonal guidance signaling by the microbiota – Xunzhong Qia – Life Sciences

Multi-hit early life adversity affects gut microbiota, brain and behavior in a sex-dependent manner – Marion Rincel – Brain, Behavior, and Immunity

Letrozole treatment of adult female mice results in a similar reproductive phenotype but distinct changes in metabolism and the gut microbiome compared to pubertal mice – Pedro J. Torres – BMC Microbiology

Supplementation of dietary non-digestible oligosaccharides from birth onwards improve social and reduce anxiety-like behaviour in male BALB/c mice – Kirsten Szklany – Nutritional Neuroscience

Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract – Dongyao Li – International Journal of Molecular Sciences

Alteration of GLP-1/GPR43 expression and gastrointestinal motility in dysbiotic mice treated with vancomycin – Xin Xu – Scientific Reports

Subchronic low-dose 2,4-D exposure changed plasma acylcarnitine levels and induced gut microbiome perturbations in mice – Pengcheng Tu – Scientific Reports

The influence of the host microbiome on 3,4-methylenedioxymethamphetamine (MDMA)-induced hyperthermia and vice versa – Emily A. Ridge – Scientific Reports

Effects of Dietary Supplementation With Enterococcus faecium and Clostridium butyricum, Either Alone or in Combination, on Growth and Fecal Microbiota Composition of Post-weaning Pigs at a Commercial Farm – Yoshiaki Sato – Frontiers in Veterinary Science

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle – Bing Wang – Frontiers in Microbiology

Intestinal dysbiosis augments liver disease progression via NLRP3 in a murine model of primary sclerosing cholangitis – Lijun Liao – Gut

 

Plant Microbiome

Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight (Phytophthora capsici) – Huixiu Li – Frontiers in Microbiology

 

Other Microbes

Preview: Strain-Level Diversity in the Gut: The P. copri Case  – Amira Metwaly – Cell Host Microbe

 

Bioinformatics and ‘-Omics’

Novel insights from uncultivated genomes of the global human gut microbiome – Stephen Nayfach – Nature

Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing – Jyun-Hong Lin – Journal of Clinical Medicine

Detection of critical antibiotic resistance genes through routine microbiome surveillance – Zachary M. Burcham – PLoS One

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations – Aleksandra I. Perz – BMC Bioinformatics

Rarity of microbial species: In search of reliable associations – Arnaud Cougoul – PLoS One

Stoplight: De novo Assembly Vastly Expands the Known Microbial Universe – Samuel S. Minot – Trends in Microbiology

 

Beneficial Microbes and Compounds

Guarana supplementation attenuated obesity, insulin resistance, and adipokines dysregulation induced by a standardized human Western diet via brown adipose tissue activation Rafael Calixto Bortolin – Phytotherapy Research

Prebiotic supplementation in frail older people affects specific gut microbiota taxa but not global diversity – Tam T. T. Tran – Microbiome

 

Water Microbiome

Composition and Dynamics of the Activated Sludge Microbiome during Seasonal Nitrification Failure – Juliet Johnston – Scientific Reports