May 21, 2019

Today’s digest is short and sweet but includes interesting articles. A brilliant essay on multidisciplinarity in microbiome research 🥰

General Microbiome

ESSAY: Multidisciplinarity in Microbiome Research: A Challenge and Opportunity to Rethink Causation, Variability, and Scale. KR Amato – BioEssays

REVIEW:Contribution of the Mucosal Microbiota to Bovine Respiratory HealthM Zeineldin. Trends in Microbiology

Characterization of a novel salt-, xylose-and alkali-tolerant GH43 bifunctional β-xylosidase/α-l-arabinofuranosidase from the gut bacterial genome. B Xu. Journal of Bioscience and Bioengineering

Gut Microbiome

Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular CarcinomaEJ Cho. Scientific Reports

The bacterial communities of the small intestine and stool in children with short bowel syndrome. SL Zeichner. PLOS ONE

Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approachesGA Lugli. BMC Genome Biology

Plant, Soil, and Water Microbiome

Microbial production and consumption of dissolved organic matter in glacial ecosystems on the Tibetan PlateauL Zhou. Water Research

Engineering banana endosphere microbiome to improve Fusarium wilt resistance in banana. Y Liu.Microbiome
Toxic responses of metabolites, organelles and gut microorganisms of Eisenia fetida in a soil with chromium contaminationR Tang. Environmental Pollution

Roles of microbes in supporting sustainable rice production using the system of rice intensificationF Doni. Applied Microbiology and Biotechnology

Cover crop species have contrasting influence upon soil structural genesis and microbial community phenotype.A Bacq-Labreuil. Scientific Reports

Preprint

Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn’s Disease Cohort . Daniel Sprockett. bioRxiv posted 19 May 2019

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May 20, 2019

This Monday, read about the stability within gut resident clonal populations of Enterobacteriaceae, significance of microbiome in personalized medicine, and impacts of intermittent supply on the drinking water microbiome. Happy reading!

General microbiome

Defining Microbiome Health through a Host Lens – Sean M. Gibbonsa – mSystems

*Review: The significance of microbiome in personalized medicine – Ava Behrouzi – Clinical and Translational Medicine

Moving towards a Robust Definition for a “Healthy” Indoor Microbiome – Karen C. Dannemiller – mSystems

Gut microbiome

*Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults – Jonathan N. V. Martinson – ISME Journal

Rectal swabs in critically-ill patients provide discordant representations of the gut microbiome compared to stool samples: a brief methodologic report – Katherine Fair – bioRxiv

Development of a Covalent Inhibitor of Gut Bacterial Bile Salt Hydrolases – Arijit A. Adhikari – bioRxiv

Temporal Gut Microbial Changes Predict Recurrent Clostridium difficile in Patients with and without Ulcerative Colitis – Allen A. Lee – boRxiv

Alteration of Gut Microbiome in Lung Cancer Patients – Li Ming – bioRxiv

Respiratory microbiome

Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in humans and ferrets – Drishti Kaul – bioRxiv

High mortality from viral pneumonia in patients with cancer – Youn-Jung Ki – Infectious Diseases

Water microbiome

Global diversity and biogeography of bacterial communities in wastewater treatment plants – Linwei Wu – Nature Microbiology

*Understanding the impacts of intermittent supply on the drinking water microbiome – Quyen Melina Bautista-de los Santos – Current Opinion in Biotechnology

Animal microbiome

Exploration of the rumen microbial diversity and carbohydrate active enzyme profile of black Bengal goat using metagenomic approach – Prashant R. Suryawanshi – Animal Biotechnology

Assessing key microbial communities determining nitrogen transformation in composting of cow manure using illumina high-throughput sequencing – Yu Sun – Waste Management

Plant/root/soil microbiome

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations – Thorsten Thiergart – bioRxiv

Response of Microbial Communities and Their Metabolic Functions to Drying–Rewetting Stress in a Temperate Forest Soil – Dong Liu – Microorganisms

Review: Rhizosphere size and shape: Temporal dynamics and spatial stationarity – Yakov Kuzyakov & Bahar S. Razavi – Soil Biology and Biochemistry

Phages and viruses

Production and characterization of novel ssRNA bacteriophage virus-like particles from metagenomic sequencing data – Ilva Lieknina – Journal of Nanobiotechnology

Techniques

PhenoGMM: Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity – Peter Rubbens – bioRxiv

May 16, 2019

Today’s digest includes the microbial communities of fruit peels, bacterial crude oil degradation, and the gut microbiome of sea cucumbers. Enjoy!

Pregnancy and early life

Preprint: Interactions between the gut microbiome and mucosal immunoglobulins A, M and G in the developing infant gut – Janzon – BioRxiv

Human gut microbiome

Evolution of the gut microbiome following acute HIV-1 infection – Rocafort – Microbiome

Animal microbiome

Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation – Yao – Evolutionary Bioinformatics

High-throughput sequencing of 16S rRNA amplicons characterizes gut microbiota shift of juvenile sea cucumber Apostichopus japonicus feeding with three antibiotics – Zhao – Journal of Oceanology and Limnology

Plant, root, and soil microbiome

Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests – Chen – Applied Microbiology and Biotechnology

Evaluation of microbial communities in peels of Brazilian tropical fruits by amplicon sequence analysis – Cruz – Brazilian Journal of Microbiology

Assembly mechanisms of soil bacterial communities in subalpine coniferous forests on the Loess Plateau, China – Zhao – Journal of Microbiology

Evaluating the effects of canine urine on urban soil microbial communities – Lee – Urban Ecosystems

Methane emission and soil microbial communities in early rice paddy as influenced by urea-N fertilization – Liu – Plant and Soil

Rhizosphere carbon supply accelerates soil organic matter decomposition in the presence of fresh organic substrates – Jackson – Plant and Soil

The relative contributions of pH, organic anions, and phosphatase to rhizosphere soil phosphorus mobilization and crop phosphorus uptake in maize/alfalfa polyculture – Sun – Plant and Soil

Diversity of anammox bacteria and abundance of functional genes for nitrogen cycling in the rhizosphere of submerged macrophytes in a freshwater lake in summer – Zhao – Journal of Soils and Sediments

Direct and indirect effects of elevated CO2 and nitrogen addition on soil microbial communities in the rhizosphere of Bothriochloa ischaemum – Xiao – Journal of Soils and Sediments

Rhizocompartments and environmental factors affect microbial composition and variation in native plants – Kang – Journal of Microbiology

The inhibitory effect of cadmium and/or mercury on soil enzyme activity, basal respiration, and microbial community structure in coal mine–affected agricultural soil – Zheng – Annals of Microbiology

Water and extremophile microbiome

Preprint: Metabolic Architecture of the Deep Ocean Microbiome – Acinas – BioRxiv

Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney – Pillot – Microbial Ecology

A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups – Shurigin – MicrobiologyOpen

Molecular analyses of bacterioplankton communities with highly abundant Vibrio clades: a case study in Bohai Sea coastal waters – Wang – Journal of Oceanology and Limnology

Archaeal communities in the deep-sea sediments of the South China Sea revealed by Illumina high-throughput sequencing – Li – Annals of Microbiology

Bacterial succession and co‐occurrence patterns of an enriched marine microbial community during light crude oil degradation in a batch reactor – Uribe‐Flores – Journal of Applied Microbiology

Microbial assemblages reflect environmental heterogeneity in alpine streams – Hotaling – Global Change Biology

Food microbiology

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal – Groenenboom – PLoS One

May 2, 2019

In today’s digest read about variations in milk and infant fecal microbiome (Ethiopia, Gambia, USA, Ghana, Kenya, Peru, Spain, and Sweden), the microbiome, metabolome, and lipidome of obese and non-obese horses (USA), and Bacteroides fragilis adaptive evolution (Western countries and China). Happy reading!

Pregnancy and birth

*What’s normal? Microbiomes in human milk and infant feces are related to each other but vary geographically: the INSPIRE study – Kimberly A. Lackey – Frontiers in Nutrition

Progesterone Increases Bifidobacterium Relative Abundance during Late Pregnancy – Meital Nuriel-Ohayon – Cell Reports

Gut microbiome

Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age – M Nazmul Huda – The Journal of nutrition

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age – Kent A. Willis – bioRxiv

*Adaptive Evolution within Gut Microbiomes of Healthy People – Shijie Zhao – Cell Host & Microbe

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders – George B. Saffouri – Nature Communications

Oral microbiome

Review: The Role of Exopolysaccharides in Oral Biofilms – C. Cugini – Journal of Dental Research

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes – Angela C. Poole – Cell Host & Microbe

Animal microbiome

*Comparison of the microbiome, metabolome, and lipidome of obese and non-obese horses – Michelle C. Coleman – PlosOne

Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning – Ubaldo De La Torre – PlosOne

Microbiome characterization of poultry products based on the poultry part and production label – Sang In Lee – FEMS Microbiology Letters

Metagenomic analysis of isolation methods of a targeted microbe, Campylobacter jejuni, from chicken feces with high microbial contamination – Junhyung Kim – Microbiome

Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health – H.Z.Sun – Journal of Dairy Science

Characterization of pig saliva as the major natural habitat of Streptococcus suis by analyzing oral, fecal, vaginal, and environmental microbiota – Kazunori Murase – PlosOne

Insight into the microbial world of Bemisia tabaci cryptic species complex and its relationships with its host – Hua-Ling Wang – Scientific Reports

Water and extremophile microbiome

The Plastisphere – Uncovering tightly attached plastic “specific” microorganisms – Inga Vanessa Kirstein – PlosOne

The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes – Han-Fei Tsao – Water Research

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities – Tim N.Enke – Current Biology

Impact of a river flood on marine water quality and planktonic microbial communities – Annamaria Zoppini – Estuarine, Coastal and Shelf Science

Microbial ecological processes in MBBR biofilms for biological phosphorus removal from wastewater – Knut Rudi – Water Science & Technology

Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany – Anita Perkins – bioRxiv

Plant/root/soil microbiome

The rice leaf microbiome has a conserved community structure controlled by complex host-microbe interactions – Veronica Roman-Reyna – bioRxiv

Spatial vs. temporal controls over soil fungal community similarity at continental and global scales – Colin Averil – The ISME Journal

Metabolomics Reveal that Engineered Nanomaterial Exposure in Soil Alters Both Soil Rhizosphere Metabolite Profiles and Maize Metabolic Pathways – Lijuan Zhao – Environmental Science: Nano

High-throughput sequencing reveals the diversity and community structure of rhizosphere fungi of Ferula Sinkiangensis at different soil depths – Tao Zhang – Scientific Reports

Microplastics can change soil properties and affect plant performance – Anderson Abel de Souza Machado – Environmental Science and Technology

April 29, 2019

Today’s Monday morning digest is about correlations of human gut microbiome with circulating metabolites, coronary artery disease severity; microbial communities in biogas plants, and proteomic profiling of gut microbiota-associated bile salt hydrolase activity.

Human gut microbiome

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

Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age – M Nazmul Huda – Journal of Nutrition

Diversification and evolution of vancomycin-resistant Enterococcus faecium during intestinal domination – Krista A. Dubin – Infection and Immunity

Microbiota as a cornerstone in the development of primary sclerosing cholangitis: paving the path for translational diagnostic and therapeutic approaches – Catherine Mooser – Gut

Alterations in the gut microbiome and metabolism with coronary artery disease severity – Honghong Liu – Microbiome

Deciphering the complex interplay between microbiota, HPV, inflammation and cancer through cervicovaginal metabolic profiling – Zehra Esra Ilhan – EBio Medicine

Relationship between gut microbiota and circulating metabolites in population-based cohorts – Dina Vojinovic – BioRxiv

Animal experiments

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

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

Plant, root, soil microbiome

Antioxidant activity changes of exopolysaccharides with different carbon sources from Lactobacillus plantarum LPC-1 and its metabolomic analysis – Xin Cheng – World Journal of Microbiology and Biotechnology

Effects of grassland afforestation on structure and function of soil bacterial and fungal communities – Kaibo Wang – Science of the Total Environment

Water microbiome and extremophiles

Effect of applied voltage and temperature on methane production and microbial community in microbial electrochemical anaerobic digestion systems treating swine manure – Jaecheul Yu – Journal of Industrial Microbiology & Biotechnology

Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants – R. Heyer – Microbiome

Techniques

Improving Assignment of Microbial Genetic Polymorphisms Assignments in Complex Samples by Bayesian Estimation – Jiarui Li – Genomics, Proteomics & Bioinformatics

Accounting for Biological Variation With Linear Mixed-effects Modelling Improves the Quality of Clinical Metabolomics Data – Kwanjeera Wanichthanarak – Computational and Structural Biotechnology Journal

Chemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity – Bibudha Parasar – ACS Central Science

Microbiome in news

Human Microbiome Therapeutics Market Research Methodology- Prominent Players Enterome Bioscience, Yakult Honsha Co. Ltd., DuPont – The Market Bureau

The Week That Wasn’t: See-Through Skulls, Fecal Soup, Microbiome Pill – Medscape

Non-Microbiology Picks

The incretin system in healthy humans: the role of GIP and GLP-1 – Jens Juul Holst – Metabolism

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 15, 2019

Today’s Monday morning digest covers reviews on different aspects of human microbiome, interesting articles about effects of early life treatments in rodents and news updates on market prediction of microbiome sequencing and therapeutics.

General microbiome

Current understanding of the human microbiome – Jack A Gilbert – Nature Communications

The Importance of the Microbiome in Bariatric Surgery: a Systematic Review – Josianne C. H. B. M. Luijten – Obesity surgery

A potential role for the gut microbiome in substance use disorders – Katherine R. Meckel – Psychopharmacology

The power of small changes: Comprehensive analyses of microbial dysbiosis in breast cancer – Sheetal Parida -Biochimica et Biophysica Acta

The lung microbiome and transplantation –  Alicia B. Mitchell – Current Opinion in Organ Transplantation

Human gut microbiome

Encrustations on ureteral stents from patients without urinary tract infection reveal distinct urotypes and a low bacterial load – Matthias T. Buhmann – Microbiome

Overuse of anti‐anaerobic drug is associated with poor post‐chemotherapy prognosis of patients with hepatocellular carcinoma – Noriho Lida – International Journal of Cancer

Antibiotic-induced shifts in fecal microbiota density and composition during hematopoietic stem cell transplantation – Sejal Morjaria – BioRxiv

Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit – AJH Cremers – BioRxiv

Animal experiments

Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior – Iva Lukić – Translational Psychiatry

Early life stress induces type 2 diabetes-like features in ageing mice – Hanna Ilchmann-Diounou – Brain, Behavior and Immunity

Early-life vancomycin treatment promotes airway inflammation and impairs microbiome homeostasis – Xin Yang – Aging

Early-life stress, microbiota, and brain development: probiotics reverse the effects of maternal separation on neural circuits underpinning fear expression and extinction in infant rats – Caitlin S.M. Cowan – Developmental Cognitive Neuroscience

Commensal Escherichia coli aggravates acute necrotizing pancreatitis through targeting intestinal epithelial cells – Junyuan Zheng – Applied and Environmental Microbiology

Host-Microbiome Synergistic Control on Sphingolipid Metabolism by Mechanotransduction in Model Arthritis – Xiaoyuan Zhou – Biomolecules

Plant, root, soil microbiome

Bacterial community diversity associated with the severity of bacterial wilt disease in tomato fields in south-east China – Xuefang Zheng – Canadian Journal of Microbiology

Bacterial disease induced changes in fungal communities of olive tree twigs depend on host genotype – Teresa Gomes – Scientific Reports

Co‐inoculation of Bacillus spp. and Pseudomonas putida at different development stages acts as a biostimulant to promote growth, yield and nutrient uptake of tomato – Yanhui He – Journal of Applied Microbiology

Water microbiome and extremophiles

Extant microbial communities in the partially desiccated Rincon de Parangueo maar crater lake in Mexico – Janet Sánchez-Sánchez – Fems Microbiology Ecology

Novosphingobium meiothermophilum sp. nov., isolated from a hot spring – Wen-Dong Xian – International Journal of Systematic and Evolutionary Microbiology

Built Environment

Impacts of Indoor Surface Finishes on Bacterial Viability – Jinglin Hu – Indoor air

Probiotics

Probiotics: If It Does Not Help It Does Not Do Any Harm. Really? – Aaron Lerner – Microorganisms

Effects of Lactobacillus plantarum PS128 on Children with Autism Spectrum Disorder in Taiwan: A Randomized, Double-Blind, Placebo-Controlled Trial – Yen-Wenn Liu – Nutrients

Microbes in the news

Global Human Microbiome Therapeutics Market Outlook 2019-2024: ENTEROME Bioscience, Rebiotix, Seres Therapeutics – NewsPrimo

Caesarean babies slower to acquire ‘good’ gut bacteria: study – PanArmenian Net

Mode of delivery has substantial impact on infants’ health – Business Standard

Newborn’s ‘Microbiome’ Could Give Clues to Weight Later – Doctors Lounge

Microbiome Sequencing Services Market is expected to grow at a CAGR of 18% during the forecast period of (2018 – 2023) – Redfield Report

Human Microbiome Market boosting the growth Worldwide – Business Herald