Category Archives: Plant Root Soil microbiome

March 28, 2018

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The impact of the microbiota on bone marrow transplantation in mice, differences in phage infection efficiency in nearly identical hosts, bacterial diversity of Brazilian artisanal cheese.

Events and jobs

Research Associate in the Department of Twin Research and Genetic Epidemiology, School of Life Cours – King’s College London

Research Associate in Department of Twin Research_School of Life Course Sciences – King’s College London

General microbiome

Variations in the relative abundance of Wolbachia in the gut of Nasutitermes arborum across life stages and castes – Michel Diouf – FEMS Microbiology Letters

Pregnancy and early life

HIV-exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohort – Shantelle Claassen-Weitz – Scientific Reports

Human respiratory microbiome

Exacerbation induces a microbiota shift in sputa of COPD patients – Eric Jubinville – PLOS ONE

Human oral microbiome

Review: Insights into the human oral microbiome – Digvijay Verma – Archives of Microbiology

Pre-print: Characterization of the salivary microbiome in people with obesity – Yujia Wu – PeerJ

Review: The oral microbiota – a mechanistic role for systemic diseases – G Jia – British Dental Journal

Human gut microbiome

Differences in epidemiological features between ulcerative colitis and Crohn’s disease: the early life-programmed versus late dysbiosis hypothesis – Laurent Beaugerie – Medical Hypotheses

Analysis of changes in intestinal flora and intravascular inflammation and coronary heart disease in obese patients – Xv Li – Experimental and Therapeutic Medicine

Animal experiments

Nutritional Support from the Intestinal Microbiota Improves Hematopoietic Reconstitution after Bone Marrow Transplantation in Mice – Anna Staffas – Cell Host & Microbe

High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats – Klaudia Bielinska – Nutrition

High salt diet exacerbates colitis in mice by decreasing Lactobacillus levels and butyrate production – Pedro M Miranda – Microbiome

The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression – Smruti Pushalkar – Cancer Discovery

Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice – Fengwei Pan – Microbiome

Deletion of choline acetyltransferase in enteric neurons results in postnatal intestinal dysmotility and dysbiosis – Carl D Johnson – The FASEB Journal

At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota – Stephen Baldwin – PLOS ONE

Impact of parenteral antimicrobial administration on the structure and diversity of the fecal microbiota of growing pigs – Mohamed Zeineldin – Microbial Pathogenesis

Pre-print: Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – bioRxiv

Pre-print: Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses – William H Palmer – bioRxiv

Proanthocyanidin‐Rich Grape Seed Extract Modulates Intestinal Microbiota in Ovariectomized Mice – Guangwen Jin – Journal of Food Science

Evaluation of the nutrition and function of cow and goat milk based on intestinal microbiota by metagenomic analysis – Zhaoxia Wang – Food & Function

Animal microbiome

Pre-print: Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding – Milica Ciric – bioRxiv

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’ – Alistair R Legione – PLOS ONE

Pre-print: Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E Dahlhausen – PeerJ

Comparison of gizzard and intestinal microbiota of wild neotropical birds – M Alexandra García-Amado – PLOS ONE

Fecal microbiota in the female prairie vole (Microtus ochrogaster) – J Thomas Curtis – PLOS ONE

Disentangling factors that shape the gut microbiota in German Shepherd dogs – Åsa Vilson – PLOS ONE

Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp – Han Liu – Microbial Biotechnology

Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring – Ursula M McCormack – mSystems

Plant, root, and soil microbiome

Tetracycline resistance genes are more prevalent in wet soils than in dry soils – Yijun Kang – Ecotoxicology and Environmental Safety

Functional diversity of ectomycorrhizal fungal communities is reduced by trace element contamination – Álvaro López-García – Soil Biology and Biochemistry

Long- and short-term effects of mercury pollution on the soil microbiome – Aline Frossard – Soil Biology and Biochemistry

Structure of surface polysaccharides from Aeromonas sp. AMG272, a plant-growth promoting rhizobacterium isolated from rice rhizosphere – Rocío Contreras Sánchez-Matamoros – Carbohydrate Research

Review: Sniffing bacterial volatile compounds for healthier plants – Rouhallah Sharifi – Current Opinion in Plant Biology

Arbuscular mycorrhizal fungi influence decomposition and the associated soil microbial community under different soil phosphorus availability – Jing Xu – Soil Biology and Biochemistry

Water and extremophile microbiome

Habitat filtering of bacterioplankton communities above polymetallic nodule fields and sediments in the Clarion-Clipperton zone of the Pacific Ocean – Markus V Lindh – Environmental Microbiology Reports

Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures – Deni Ribicic – Marine Pollution Bulletin

Built environment

Pre-print: Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials – Marja I Roslund – PeerJ

Food microbiology

Interspecies variation in biofilm-forming capacity of psychrotrophic bacterial isolates from Chinese raw milk – Lei Yuan – Food Control

Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons – Mayra Carla de Freitas Martins – Food Research International

Probiotics/prebiotics

Salecan stabilizes the microstructure and improves the rheological performance of yogurt – Renjie Fu – Food Hydrocolloids

Probiotic Lactobacillus casei Zhang (LCZ) alleviates respiratory, gastrointestinal & RBC abnormality via immuno-modulatory, anti-inflammatory & anti-oxidative actions – Yan-Yan Hor – Journal of Functional Foods

Routine Supplementation of Lactobacillus rhamnosus GG and Risk of Necrotizing Enterocolitis in Very Low Birth Weight Infants – Andrea F Kane – The Journal of Pediatrics

Phages and viruses

Continued Need for Comprehensive Genetic and Phenotypic Characterization of Viruses: Benefits of Complementing Sequence Analyses with Functional Determinations – Aaron C Brault – The American Journal of Tropical Medicine and Hygiene

Detection of Hantaviruses and Arenaviruzses in three-toed jerboas from the Inner Mongolia Autonomous Region, China – Zhiqiang Wu – Emerging Microbes & Infections

Enteric Virome Sensing—Its Role in Intestinal Homeostasis and Immunity – Rebecca N Metzger – Viruses

Commentary: Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome – Blessing O Anonye – Frontiers in Cellular and Infection Microbiology

Multiple mechanisms drive phage infection efficiency in nearly identical hosts – Cristina Howard-Verona – The ISME Journal

Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples – Virginie Sauvage – PLOS ONE

A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa – Marike Geldenhuys – PLOS ONE

Pre-print: Ecological and evolutionary consequences of viral plasticity – Melinda Choua – bioRxiv

Bioinformatics

Pre-print: Taxonomy annotation errors in 16S rRNA and fungal ITS sequence databases – Robert C Edgar – bioRxiv

Metabolomics

Analysis of paper foxing by newly available omics techniques – Justyna Szulc – International Biodeterioration & Biodegradation

Review: Targeting human urinary metabolome by LC–MS/MS: a review – Jose Rodríguez-Morató – Bioanalysis

GC-MS Based Metabolomics and NMR Spectroscopy Investigation of Food Intake Biomarkers for Milk and Cheese in Serum of Healthy Humans – Alessia Trimigno – Metabolites

Techniques

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples – Jeremiah J Minich – mSystems

eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems – Ihsanul Khaliq – FEMS Microbiology Ecology

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species – Xia Liu – Preparative Biochemistry and Biotechnology

More microbes

Review: New therapeutics from Nature: The odd case of the bacterial cytotoxic necrotizing factor 1 – Zaira Maroccia – Biomedicine & Pharmacotherapy

Pre-print: An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition – Karthik Hullahalli – bioRxiv

Microbes in the news

Here’s Why Antibiotics May Give Viruses a Leg Up – Christopher Wanjek – Live Science

‘Nanobot’ viruses tag and round up bacteria in food and water – Carolyn Wilke – ScienceNews

Your rubber ducky is probably crawling with bacteria, scientists say – STAT

Newly discovered bacteria can break down biomass – Phys.Org

Microbes on the market

Biocodex funds microbiome research on link between diet, colon cancer, IBD – Healio

Rebiotix’s Lee Jones to Receive TRUST 2018 Courageous Women in Health Care Award – PR Newswire

March 24, 2018

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Events and jobs
Senior Phage Display Scientist: Antibodies – Cambridgeshire, England – Paramount Recruitment

General microbiome
Metagenomic mining of regulatory elements enables programmable species-selective gene expression – Nathan I Johns – Nature Methods

Pregnancy and early life
Seeding of the Fetal Gut Microbiome: Insights Into Origins and Significance – LF Stinson – Journal of Paediatrics and Child Health

Evidence of dysbiosis in the intestinal microbial ecosystem of children and adolescents with primary hyperlipidemia and the potential role of regular hazelnut intake. – Giorgio Gargari – Fems Microbiology Ecology

Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century – Bethany M Henrick – Msphere

Multi-site human microbiome
Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier. – Lesley Hoyles – Microbiome

Human vaginal microbiome
Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in China – Hongwei Zhang – Scientific Reports

Human nearly-sterile sites (blood, organs, brain)

Human gut microbiome
The current state and future direction of DoD gut microbiome research: a summary of the first DoD gut microbiome informational meeting – Steven Arcidiacono – Standards in Genomic Sciences

Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders. – Joby Pulikkan – Microbial Ecology

An Aberrant Microbiota is not Strongly Associated with Incidental Colonic Diverticulosis. – Roshonda B Jones – Scientific Reports

Untargeted metabolomics identifies trimethyllysine, a TMAO-producing nutrient precursor, as a predictor of incident cardiovascular disease risk. – Xinmin S Li – Jci Insight

Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis – Xinyue Huang – IOVS

Microbial interactions
Cell death as a trigger for morphogenesis. – Boris Aguilar – Plos One

Horizontal Gene Transfer Building Prokaryote Genomes: Genes Related to Exchange Between Cell and Environment are Frequently Transferred – Apuã C. M. Paquola – Journal of Molecular Evolution

Animal experiments
Preprint: Social communication between microbes colonizing the social honey bee Apis mellifera – Irene Newton – bioRxiv

Dietary butyrate glycerides modulate intestinal microbiota composition and serum metabolites in broilers – Xiaojian Yang – Scientific Reports

Bacterial lactase genes diversity in intestinal mucosa of mice with dysbacterial diarrhea induced by antibiotics – Chengxing Long – 3 Biotech

Allelic variation in a single genomic region alters the microbiome of the snail Biomphalaria glabrata. – Euan R O Allan – The Journal Of Heredity

Tall oil fatty acid inclusion in the diet improves performance and increases ileal density of Lactobacilli spp. in broiler chickens. – K Vienola – British Poultry Science

Effects of dietary Bacillus amyloliquefaciens supplementation on growth performance, intestinal morphology, inflammatory response, and microbiota of intra-uterine growth retarded weanling piglets – Yue Li – Journal Of Animal Science And Biotechnology

Temperature-Dependent Effects of Cutaneous Bacteria on a Frog’s Tolerance of Fungal Infection. – Matthew J Robak – Frontiers In Microbiology

Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice. – Fengwei Pan – Microbiome

Animal microbiome
Review: The mosquito holobiont: fresh insight into mosquito-microbiota interactions – Morgane Guégan – Microbiome

Plant, root, and soil microbiome
Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields – Kunkun Fan – Soil Biology and Biochemistry

Seasonal Effects on Microbial Community Structure and Nitrogen Dynamics in Temperate Forest Soil – Tomohiro Yokobe – forests

High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China. – Yu-Jie Wei – Plos One

Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities. – Annelein Meisner – Frontiers In Microbiology

Vanillic acid changed cucumber (Cucumis sativus L.) seedling rhizosphere total bacterial, Pseudomonas and Bacillus spp. communities. – Xingang Zhou – Scientific Reports

Review: Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences. – Mohammadhossein Ravanbakhsh – Microbiome

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. – E Gonzalez – Microbiome

Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture – Nicholas Ozede Igiehon – Int. J. Environ. Res. Public Health

Vascular plant-mediated controls on atmospheric carbon assimilation and peat carbon decomposition under climate change – Konstantin Gavazov – Global Change Biology

Water and extremophile microbiome
Preprint: Dynamics and interactions of highly resolved marine plankton via automated high frequency sampling – David M. Needham – bioRxiv

Bioremediation of PCB-contaminated shallow river sediments: The efficacy of biodegradation using individual bacterial strains and their consortia. – Hana Horváthová – Chemosphere

Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community – Xavier Mayali – FEMS Microbiology Ecology

Built environment
Community Structure Analysis and Biodegradation Potential of Aniline-Degrading Bacteria in Biofilters – Luanfeng Hou – Current Microbiology

Food microbiology
Review: The influence of diet on anti-cancer immune responsiveness – Laura Soldati – Journal of Translational Medicine

The Efficacy of a Chewing Gum Containing Phyllanthus emblica Fruit Extract in Improving Oral Health. – Ya-Ting Chuang – Current Microbiology

Review: The Microbial Diversity of Sherry Wines – Gustavo Cordero-Bueso – Fermentation

Probiotics / prebiotics / antibiotics
The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster – Khachik E. Labachyan – Gut Pathogens

Bacillus clausii inhibits bone loss by skewing Treg-Th17 cell equilibrium in postmenopausal osteoporotic mice – Hamid Y. Dar – Nutrition

Prebiotic Potential of Herbal Medicines Used in Digestive Health and Disease. – Christine Tara Peterson – Journal Of Alternative And Complementary Medicine (New York, N.Y.)

Phages and viruses
Identification of Novel Viruses in Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks – Rafal Tokarz – Msphere

Microbes in the news
Skin spray heals US woman’s flesh-eating bacteria wounds – Alice Klein – New Scientist

March 23, 2018

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Optogenetic regulation of transcription to promote biosynthesis of desired chemicals from fungi, the effect of yeast and bacteria on floral nectar, guidelines and best practices for human microbiome sampling/sequencing/processing.

Plant, root, and soil microbiome

Evaluation of conventional and response surface level optimisation of n-dodecane (n-C12) mineralisation by psychrotolerant strains isolated from pristine soil at Southern Victoria Island, Antarctica – Syahir Habib – Microbial Cell Factories

Analysis of microbiota in bellflower root, Platycodon grandiflorum, obtained from South Korea – Daeho Kim – Journal of Microbiology and Biotechnology

Contrasting effects of yeasts and bacteria on floral nectar traits – Rachel L Vannette – Annals of Botany

Water and extremophile microbiome

Mechanisms of Methyl Mercury Net Degradation in Alder Swamps: The Role of Methanogens and Abiotic Processes – Rose-Marie Kronberg – Environmental Science & Technology Letters

Microbial mat of the thermal springs Kuchiger Republic of Buryatia: species composition, biochemical properties and electrogenic activity in biofuel cell – Denis Aleksandrovich Yuriev – IOP Conference Series: Earth and Environmental Sciences

Bioinformatics

Pre-print: A comprehensive automated pipeline for human microbiome sampling, 16S rRNA gene sequencing and bioinformatics processing – Luisa W Hugerth – bioRxiv

Pre-print/Review: Real-time analysis and visualization of pathogen sequence data – Richard A Neher – bioRxiv

Techniques

Yeast Biofilm as a Bridge Between Medical and Environmental Microbiology Across Different Detection Techniques – Luca Roscini – Infectious Diseases and Therapy

More microbes

Optogenetic regulation of engineered cellular metabolism for microbial chemical production – Evan M Zhao – Nature

Pre-print: Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators – Benjamin Hommel – bioRxiv

Pre-print: High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions – Rieza Aprianto – bioRxiv

Pre-print: Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39 – Jelle Slager – bioRxiv

Microbes in the news

Oral microbiome and anthropometry changes following caries arrest using silver-nitrate/fluoride-varnish – EurekAlert

Metagenomics of early childhood oral health and early childhood caries – EurekAlert

Synergistic effects of smoking and obesity on the subgingival microbiome – EurekAlert

Gut bacteria can mean life or death for birds – EurekAlert

Its name is LUCA. Now it’s needing second thoughts – Stephen Fleischfresser – Cosmos

Plants really do feed their friends – ScienceDaily

Bacteria eats greenhouse gas with a side of protein – Phys.org

Survival of the Slimiest: The Persistent Nature of Biofilms – Sonali D Advani – Medscape

Amy’s non-microbiology picks

Editorial: Asymmetry symposium unites economists, physicists and artists – Nature

March 22, 2018

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Of special note today: A randomized double blind controlled clinical trial on the impacts of probiotics on Alzheimer’s demonstrated an improvement in cognitive function, triglycerides, insulin sensitivity and C reactive protein; and a meta-analysis of the lung microbiome in tuberculosis identified specific species that are characteristic of the disease.

Events and jobs

Research Associate – Kintai Therapeutics – Cambridge, MA

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Human respiratory microbiome

*Meta-analysis of the lung microbiota in pulmonary tuberculosis – Bo-young Hong – Tuberculosis

Human skin microbiome

Longitudinal study of the psoriasis-associated skin microbiome during therapy with ustekinumab in a randomized Phase 3b clinical trial – Michael Loesche – Journal of Investigative Dermatology

Human oral microbiome

The subgingival microbiome in patients with established rheumatoid arthritis – Ted R Mikuls – Rheumatology

Self-reported bovine milk intake is associated with oral microbiota composition – Ingegerd Johansson – PLOSone

Human uro-genital microbiome

A Distinctive Urinary Metabolomic Fingerprint Is Linked With Endoscopic Postoperative Disease Recurrence in Crohn’s Disease Patients – Ammar Hassanzadeh Keshteli – Inflammatory Bowel Diseases

Human gut microbiome

Review: Interrelation of Diet, Gut Microbiome, and Autoantibody Production – Ioanna Petta – Frontiers in Immunology

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Animal experiments

Microbiome-metabolome signatures in mice genetically prone to develop dementia, fed a normal or fatty diet – Elena Sanguinetti – Scientific Reports

Influence of dietary protein and fructooligosaccharides on fecal fermentative end-products, fecal bacterial populations and apparent total tract digestibility in dogs – Carlo Pinna – BMC Veterinary Research

Animal microbiome

Review: The tripartite interactions between the mosquito, its microbiota and Plasmodium – Ottavia Romoli – BMC Parasites & Vectors

Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development – XiaoLi Bing – mBio

Lower dietary concentrate level increases bacterial diversity in the rumen of Cervus elaphus yarkandensis – Wenxi Qian- Canadian Journal of Microbiology

Evaluation of milk sample fractions for characterization of milk microbiota from healthy and clinical mastitis cows – Svetlana Ferreira Lima – PLOSone

Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E. Dahlhausen – PeerJ

Effects of high ambient temperature on the community structure and composition of ileal microbiome of broilers – X J Wang – Poultry Science

Oscillating bacterial expression states generate herd immunity to viral infection – Christopher J. R. Turkington – bioRxiv

Plant, root, and soil microbiome

High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits – Marta Maciejewska – Antibiotics

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly – Kateryna Zhalnina – Nature Microbiology

Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms – Ma del Carmen Orozco-Mosqueda – Microbiological Research

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere – Hector Urbina – Fungal Biology

Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on Earth – Terry J. McGenity – The ISME Journal

Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system – Ilonka C. Engelhardt – The ISME Journal

Water and extremophile microbiome

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition – Geoff A. Christensen – PLOSone

Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre – Kyle R Frischkorn – The ISME Journal

Microbial parasites make cyanobacteria blooms less of a trophic dead end than commonly assumed – Matilda Haraldsson – The ISME Journal

Air Microbiome

Deposition rates of viruses and bacteria above the atmospheric boundary layer
– Isabel Reche – The ISME Journal

Microbial Ecology

Review: Understanding Microbiome Stability in a Changing World – Ashley Shade – mSystems

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Probiotics / prebiotics

*Effect of Probiotic Supplementation on Cognitive Function and Metabolic Status in Alzheimer’s Disease: A Randomized, Double-Blind and Controlled Trial – Elmira Akbari – Frontiers in Aging Neuroscience

Bioinformatics

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes – Joel A Boyd – Nucleic Acids Research

VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing – Hiroshi Mori – BMC Systems Biology

Machine learning for tackling microbiota data and infection complications in immunocompromised patients with cancer – J. Luis Espinoza – Journal of Internal Medicine

A highly adaptive microbiome-based association test for survival traits – Hyunwook Koh – BMC Genomics

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Microbes in the news

Making intricate images with bacterial communities – Psy.Org

Many Non-Antibiotic Drugs Affect Gut Bacteria. A new study finds that more than 200 human-targeted, non-antibiotic drugs inhibit the growth of bacterial species that make up part of the human microbiome – Catherine Offord

‘New life form’ answers question about evolution of cells – Science Daily

Bacteria and Art

This watercolour painting was created by artistic bacteria – Sarah Roberts had a germ of an idea: let bacteria take creative control – Anna Marks – Wired

Crocheted and Embroidered Bacteria Grow in Elin Thomas’s Fiber Art Petri Dishes – Laura Staugaitis – Colossal

 

March 21, 2018

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A long digest today – lots of science on the gut, environment, and some interesting editorials on techniques, bioinformatics, and methodologies applied to microbiome studies.

General microbiome

[pre print] Oscillating bacterial expression states generate herd immunity to viral infection – Christopher J. R. Turkington – bioRxiv

Retraction: Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – The PLOS ONE Editors – PLOS ONE

DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy – Elisa Banchi – PLOS ONE

Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome – Zachary S. Ballard – ACS Nano

Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease – Catherine A. Lozupone – mSystems

Making Millennial Medicine More Meta – Peter J. Turnbaugh – mSystems

Pregnancy and early life

Neonatal intestinal dysbiosis in necrotizing enterocolitis – Naomi-Liza Denning – Molecular Medicine

Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units – Zhi-Hui Zou – Annals of Clinical Microbiology and Antimicrobials

* The Effect of Early Limited Formula on Breastfeeding, Readmission, and Intestinal Microbiota: A Randomized Clinical Trial – Valerie J. Flaherman – The Journal of Pediatrics

Multi-site human microbiome

The Complex Interplay between Chronic Inflammation, the Microbiome, and Cancer: Understanding Disease Progression and What We Can Do to Prevent It – Heather Armstrong – Cancers

Human oral microbiome

Salivary microbial profiles in relation to age, periodontal, and systemic diseases – Ronaldo Lira-Junior – PLOS ONE

Human respiratory microbiome

Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective – Georgios D. Kitsios – mSystems

Host-Microbe Interactions in Airway Disease: toward Disease Mechanisms and Novel Therapeutic Strategies – Emily K. Cope – mSystems

Human gut microbiome

The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome – Christopher John Kiely – Gut Microbes

Species Level Description of the Human Ileal Bacterial Microbiota – Heidi Cecilie Villmones – Nature

* Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates – Francesco Multinu – mSphere

* Extensive impact of non-antibiotic drugs on human gut bacteria – Lisa Maier – Nature

In this issue: Effect of gut microbiome on mucosal immunity and enteric diseases – Kumar, Himanshu – International Reviews of Immunology

Characterization of intestinal microbiota in alcoholic patients with and without alcoholic hepatitis or chronic alcoholic pancreatitis – Dragos Ciocan – Nature

Clostridium difficile Exposures, Colonization, and the Microbiome: Implications for Prevention – Sara L. Revolinski – Infection Control and Hospital Epidemiology

* Of Microbes and Minds: A Narrative Review on the Second Brain Aging – Riccardo Calvani – Frontiers in Medicine

Microbiome: Viral hormones activate human insulin signalling – Ashley York – Nature

Modulation of Gut Microbiota: A Novel Paradigm of Enhancing the Efficacy of Programmed Death-1 and Programmed Death Ligand-1 Blockade Therapy – Yiming Wang – Frontiers in Immunology

* Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study – Carmen Losasso – Frontiers in Microbiology

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies – Melanie Tramontano – Nature

Animal experiments

Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E. Dahlhausen – PeerJ

Low dose brain estrogen prevents menopausal syndrome while maintaining the diversity of the gut microbiomes in estrogen-deficient rats – Sunmin Park – American Journal of Physiology-Endocrinology and Metabolism

Oral supplementation of Bifidobacterium longum strain BR-108 alters cecal microbiota by stimulating gut immune system in mice irrespectively of viability – Yuko Makioka – Bioscience, Biotechnology, and Biochemistry

Animal microbiome

Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok – Martha Zakrzewski – Nature

Changes in Larval Mosquito Microbiota Reveal Non-target Effects of Insecticide Treatments in Hurricane-Created Habitats – Joseph P. Receveur – Microbial Ecology

Dissecting cause and effect in host-microbiome interactions using the combined worm-bug model system – Marina Ezcurra – Biogerontology

Plant, root, and soil microbiome

[pre print] Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ pre prints

Changes in the Metagenome of Prokaryotic Community as an Indicator of Fertility of Arable Soddy-Podzolic Soils upon Fertilizer Application – A. N. Naliukhin – Eurasian Soil Science

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification – Jun Lou – PeerJ

Plant growth-promoting rhizobacteria associated with avocado display antagonistic activity against Phytophthora cinnamomi through volatile emissions – Alfonso Méndez-Bravo – PLOS ONE

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields – Xuhong Song – PLOS ONE

Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6 – Betina Cecilia Agaras – PLOS ONE

Water and extremophile microbiome

Microbial communities underpinning mesophilic anaerobic digesters treating food wastewater or sewage sludge: a full-scale study – Joonyeob Lee – Bioresource Technology

Bacteria from Antarctic environments: diversity and detection of antimicrobial, antiproliferative, and antiparasitic activities – Tiago R. Silva – Polar Biology

Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought – Debra A. Davis – Microorganisms

Diversity and assembly patterns of activated sludge microbial communities: A review – Yu Xia – Biotechnology Advances

Temperature-induced changes in a microbial community under autotrophic denitrification with sulfide – Michal Sposob – Process Biochemistry

Metagenomic Exploration of Microbial Signatures on Periyar River Sediments from the Periyar Tiger Reserve in the Western Ghats – Aparna Chakkamadathil Rajeev – Genome Announcements

Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes – Ian Hewson – PLOS One

Shifts in dissolved organic matter and microbial community composition are associated with enhanced removal of fecal pollutants in urban stormwater wetlands – Xiao Huang – Water Research

Effect of semi-permeable cover system on the bacterial diversity during sewage sludge composting – Tatiana Robledo-Mahón – Journal of Environmental Management

* Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth? – S. K. Schmidt – Antonie van Leeuwenhoek

Rapid alterations to marine microbiota communities following an oil spill – Brad J. Gemmell – Ecotoxicology

Microbial communities and their potential for degradation of dissolved organic carbon in cryoconite hole environments of Himalaya and Antarctica – Aritri Sanyal – Microbiological Research

Built environment

Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms – John A. Handley – Frontiers in Microbiology

Food microbiology

Characterization of Bacteria in Nigerian Yogurt as Promising Alternative to Antibiotics in Gastrointestinal Infections – Anthony Opeyemi Ayeni – Journal of Dietary Supplements

Probiotics / prebiotics

Polyphenols’ Gut Microbiota Metabolites: Bioactives or Biomarkers? -Francisco A. Tomas-Barberan – Journal of Agriculture and Food Chemistry

* A Multi-strain Probiotic Reduces the Fatty Liver Index, Cytokines and Aminotransferase levels in NAFLD Patients: Evidence from a Randomized Clinical Trial – Nazarii Kobyliak – Journal of Gastrointestinal and Liver Diseases

Bioinformatics

Species classifier choice is a key consideration when analysing low-complexity food microbiome data – Aaron M. Walsh – Microbiome

Data and Statistical Methods To Analyze the Human Microbiome – Levi Waldron – mSystems

* Discovery of enzymes for toluene synthesis from anoxic microbial communities – Beller HR – Nature

Techniques

Community Assembly Processes of the Microbial Rare Biosphere – Xiu Jia – Trends in Microbiology

* Metabolomics: A High-Throughput Platform for Metabolite Profile Exploration – Jing Cheng – Computational Systems Biology

[Patent] Spectrometric Analysis of Microbes – Zoltan Takats

* Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics – Stefan A. Boers – European Journal of Clinical Microbiology & Infectious Diseases

Comparative analysis of four commercial on-farm culture methods to identify bacteria associated with clinical mastitis in dairy cattle – Jair C. Ferreira – PLOS One

Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics – Casey M. Theriot – mSystems

Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research – Nicole A. Hynson – mSystems

Microbiomes In Natura: Importance of Invertebrates in Understanding the Natural Variety of Animal-Microbe Interactions – Jillian M. Petersen – mSystems

Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies – Isabelle Laforest-Lapointe – mSystems

Microbes on the market 

DuPont Expands Microbiome Research Program, Adds Second Partnership with Fermentation Specialist

Science, publishing, and career

Biocodex Microbiota Foundation Awards Grants to Two Innovative Researchers in the Microbiome Field

Early-Career Systems Microbiology Scientists – Jack A. Gilbert – mSystems

Ed’s non-microbiology picks (can use your own name of course!) (cool non-microbiology science)

Self-employed people happier and more engaged at work, study finds

Health Care Spending in the United States and Other High-Income Countries

Ancient DNA Is Rewriting Human (and Neanderthal) History

Sturdy Insulator Made of Wood

How exercise in old age prevents the immune system from declining

March 15, 2018

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A few interesting articles in early life human microbiome, plus:
A comparison between Staphylococcus epidermidis commensal and pathogenic lineages from the skin of healthy individuals living in North American and India; A new tool to reconstruct microbial genome-scale metabolic models (GSMMs) from their genome sequence; The seasonal changes in Amazon rainforest soil microbiome are associated with changes in the canopy; A specific class of chemicals secreted by birds modulates their feather microbiome; chronic stress alters gut microbiota and triggers a specific immune response in a mouse model of colitis; and evidence that the short chain fatty acids profile in the gut reflects the impact of dietary fibre on the microbiome using the PolyFermS continuous intestinal fermentation model.

Pregnancy and early life

*Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium – Terhi Tapiainen – Pediatric Research

*Bifidobacterium longum subsp infantis CECT7210 supplemented formula reduces diarrhoea in healthy infants: a randomized controlled trial – Joaquin Escribano – Pediatric Research

*Gut microbiota in adolescents and the association with fatty liver: The EPOCH study – Maggie A Stanislawski – Pediatric Research

Review: Does Dysbiosis in Intestinal Microbiome Plays a Role in Children with Relapsing Idiopathic Nephrotic Syndrome? – Crespo-Salgado J. – American Journal of Nephrology

Gut Microbiota Dysbiosis in Children with Relapsing Idiopathic Nephrotic Syndrome – Tsuji S – American Journal of Nephrology

Human skin microbiome

*Phylogenomic Based Comparative Studies on Indian and American Commensal Staphylococcus epidermidis Isolates – Shikha Sharma – Frontiers in Microbiology

Human oral microbiome

Unusual oral mucosal microbiota after hematopoietic cell transplantation with glycopeptide antibiotics: potential association with pathophysiology of oral mucositis – Misato Muro – Folia Microbiologica

Supragingival and subginival microbiota from patients with poor oral hygiene submitted to radiotherapy for head and neck cancer treatment – Elerson Gaetti-Jardim Jr – Archives of Oral Biology

Human nearly-sterile sites

PrePrint: Transcriptome analysis in whole blood reveals increased microbial 1 diversity in schizophrenia – Loes M Olde Loohuis – bioRxiv

Human gut microbiome

Investigations on the interplays between Schistosoma mansoni, praziquantel and the gut microbiome – Pierre H. H. Schneeberger – Parasites and Vectors

FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects – Williams Turpin – Gut Microbes

Bacterial growth, flow, and mixing shape human gut microbiota density and composition – Markus Arnoldini – Gut Microbes

Complementary effects of cereal and pulse polyphenols and dietary fiber on chronic inflammation and gut health – Joseph M. Awika – Food & Function

Roseburia intestinalis alleviates experimental colitis pathology by inducing anti-inflammatory responses – Zhaohua Shen – Gastroenterology and Hepatology

Targeting gut microbiota in hepatocellular carcinoma: probiotics as a novel therapy – Murphy L. Y. Wan – Hepatobiliary Surgery and Nutrition

Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients – Matthew K. Doherty – mBio

Disruption of the Gut Microbiota With Antibiotics Exacerbates Acute Vascular Rejection
Kevin Rey – Transplantation

Review: Multiple hit infection and autoimmunity: the dysbiotic microbiota–ACPA connection in rheumatoid arthritis – Lazaros I Sakkas – Current Opinion in Rheumatology

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In vitro experiments

*Understanding the prebiotic potential of different dietary fibers using an in vitro continuous adult fermentation model (PolyFermS) – Sophie A. Poeker – Scientific Reports

Animal experiments

Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka – Cell Reports

Fructose liquid and solid formulations differently affect gut integrity, microbiota composition and related liver toxicity: a comparative in vivo study – Raffaella Mastrocola – Journal of Nutritional Biochemistry

NLRX1 Modulates Immunometabolic Mechanisms Controlling the Host–Gut Microbiota Interactions during Inflammatory Bowel Disease – Andrew Leber – Frontiers in Immunology

Tapering Courses of Oral Vancomycin Induce Persistent Disruption of the Microbiota that Provide Colonization Resistance to Clostridium difficile and Vancomycin-Resistant Enterococci in Mice – Myreen E. Tomas – Antimicrobial Agents and Chemotherapy

The Lung Microbiota of Healthy Mice are Highly Variable, Cluster by Environment, and Reflect Variation in Baseline Lung Innate Immunity – Robert P. Dickson – American Journal of Respiratory and Critical Care Medicine

Interactions between stress and sex in microbial responses within the microbiota-gut-brain axis to stress in a mouse model – Matthew C.B. Tsilimigras – Psychosomatic Medicine

*Chronic stress promotes colitis by disturbing the gut microbiota and triggering immune system response – Xinghua Gao – PNAS

Modulation of inflammatory arthritis by gut microbiota through mucosal inflammation and autoantibody generation – Widian K. Jubair – Arthritis & Rheumatology

Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers – Helen M. Golder

Animal microbiome

Gut microbes limit growth in house sparrow nestlings (Passer domesticus) but not through limitations in digestive capacity – Kevin D. Kohl – Integrative Zoology

*Chemical regulation of body feather microbiota in a wild bird – Staffan Jacob – Molecular Ecology

Plant, root, and soil microbiome

Bacterial community changes in response to oil contamination and perennial crop cultivation – Lijuan Yan – Environmental Science and Pollution Research

Integrated network analysis reveals the importance of microbial interactions for maize growth – Jiemeng Tao – Applied Microbiology and Biotechnology

*Spatio-temporal dynamics of soil bacterial communities as a function of Amazon forest phenology – Erika Buscardo – Scientific Reports

Microbiome dynamics during ensiling of corn with and without Lactobacillus plantarum inoculant – Jitendra Keshridf – Applied Microbiology and Biotechnology

Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture – Linkun Wu – International Journal of Molecular Sciences

Chrysomya megacephala larvae feeding favourably influences manure microbiome, heavy metal stability and greenhouse gas emissions – Xiaoyun Wang – Microbial Biotechnology

Water and extremophile microbiome

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community – Laura Gómez-Consarnau – bioRxiv

Microbial Ecology

Mycotoxin: Its Impact on Gut Health and Microbiota – Winnie-Pui-Pui Liew – Frontiers in Cellular and Infection Microbiology

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Probiotics / prebiotics

Effect of an Enterococcus faecium probiotic on specific IgA following live Salmonella Enteritidis vaccination of layer chickens – Breno C. B. Beirão – Avian Pathology

Effect of a Protein Supplement on the Gut Microbiota of Endurance Athletes: A Randomized, Controlled, Double-Blind Pilot Study – Diego Moreno-Pérez – Nutrients

Fecal Transplants

Fecal transplants in spondyloarthritis and uveitis: ready for a clinical trial? – Rene Y Choi – Current Opinion in Rheumatology

Phages and viruses

Together Forever: Bacterial–Viral Interactions in Infection and Immunity – Zhenda Shi – Viruses

Bioinformatics

*Towards predicting the environmental metabolome from metagenomics with a mechanistic model – Daniel R. Garza – Nature Microbiology

Phylogenetic convolutional neural networks in metagenomics – Diego Fioravanti – BMC Bioinformatics

Waste and Pollution

Illumina MiSeq Sequencing reveals microbial community in HA process for dyeing wastewater treatment fed with different co-substrates – Xuehui Xie – Chemosphere

Techniques

Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis – Jocelyn Sietsma Penington – Scientific Reports

Direct detection of Coccidioides from Arizona soils using CocciENV, a highly sensitive and specific real-time PCR assay – J R Bowers – Medical Mycology

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March 14, 2018

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Today’s Digest adds to the growing literature of microbiome research. Highlights include the synergistic relationship between fungi and an invasive plant, enteral nutrition may help maintain the gastrointestinal function of critically ill patients, and the NCI calls for advancing epidemiologic research on the human microbiome.

Jobs

Student Trainee Microbiology Student Trainee Usda Pathways Internship Program Job in SAINT LOUIS, MO – Opening from 3/12-3/16, 2018

General microbiology

Antibiotic-induced population fluctuations and stochastic clearance of bacteria – Jessica Coates et al. – eLife

Press: Biophysicists discover how small populations of bacteria survive treatment – Science Daily

Preprint: Division of labor during biofilm matrix production – Anna Dragos et al. – bioRxiv

Isolation and characterization of two novel groups of kanamycin-resistance ColE1-like plasmids in Salmonella enterica serotypes from food animals – Chin-Yi Chen et al. – PLoS One

Human nasal microbiome

Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities – Yaqi You et al. – PLoS One

Human oral microbiome

In vitro: pH changes of mixed biofilms of Streptococcus mutans and Candida albicans after exposure to sucrose solutions in vitro – Thamires Priscila Cavazana et al. – Archives of Oral Biology

Human lung microbiome

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis – Lisa A. Carmody et al. – PLoS One

Human gut microbiome

** Review: Effects of enteral nutrition on gastrointestinal function in patients who are critically ill – Michael Schörghuber and Sonja Fruhwald – The Lancet Gastroenterology & Hepatology

An overview on the interplay between nutraceuticals and gut microbiota – Adrian Catinean et al. – PeerJ

Animal experiments

Aronia berry (Aronia mitschurinii ‘Viking’) inhibits colitis in mice and inhibits T cell tumour necrosis factor-α secretion – Derek A. Martin et al. – Journal of Functional Foods

Mouse: Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka et al. – Cell Reports

Animal microbiome

Pathology and bacteria related to digital dermatitis in dairy cattle in all year round grazing system in Brazil – Tiago F. Moreira et al. – PLoS One

Food microbiology

The potential use of leaf extracts of two Newtonia (Fabaceae) species to treat diarrhoea – K.E. Motlhatlego et al. – South African Journal of Botany

Editorial: The interactions between food components and human nutrition – Charles Brennan – International Journal of Food Science & Technology

Plant, root and soil microbiome

** The unspecificity of the relationships between the invasive Pennisetum setaceum and mycorrhizal fungi may provide advantages during its establishment at semiarid Mediterranean sites – G. Rodríguez-Caballero et al. – Science of the Total Environment

Review: Environmental and public health related risk of veterinary zinc in pig production – Using Denmark as an example – John Jensen et al. – Environment International

Hydrophobins contribute to root colonization and stress responses in the rhizosphere-competent insect pathogenic fungus Beauveria bassiana – Soumya Moonjely et al. – Microbiology

Perspective: Tracing the role of human civilization in the globalization of plant pathogens – Alberto Santini et al. – ISME

Water and extremophile microbiome

Review: Surface water flooding, groundwater contamination, and enteric disease in developed countries: A scoping review of connections and consequences – L. Andrade et al. – Environmental Pollution

Domestic wastewater treatment and power generation in continuous flow air-cathode stacked microbial fuel cell: Effect of series and parallel configuration – Edson Baltazar Estrada-Arriaga et al. – Journal of Environmental Management

Effect of particle size and heterogeneity on sediment biofilm metabolism and nutrient uptake scaled using two approaches – Samuel P. Parker et al. – Ecosphere

Phages and viruses

Differential impact of lytic viruses on prokaryotic morphopopulations in a tropical estuarine system (Cochin estuary, India) – Vijayan Jasna et al. – PLoS One

Bioinformatics

A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data – Juhee Lee and Marilou Sison-Mangus – Frontiers in Microbiology

A systems pharmacology model for inflammatory bowel disease – Violeta Balbas-Martinez et al. – PLoS One

Microbes in the news

** Of Microbes and Men: Advancing Epidemiologic Research on the Human Microbiome – Victoria Fisher – National Cancer Institute

Opinion: Inflammatory bowel disease: complexity and variability need integration – Claudio Fiocchi – Frontiers in Medicine

Stress: How social conflict alters gut bacteria – Maria Cohut – Medical News Today

High-Fiber Generates Gut Bacteria Good for Type 2 Diabetes – Becky McCall – Medscape

New pathway may lead to improved probiotic products – Tim Lundeen – Feedstuffs

Probiotic potential: Specific gut microbes could cut severity of parasitic infections in developing countries – Nathan Gray – NUTRAingredients

Wandering Gut Bacteria Could Be Behind Conditions Like Lupus – Abby Norman – Futurism

Model Can Predict Which Bacteria will Engraft after FMT – Rachel Lutz – MD Magazine

Can Coral Microbes Protect Reefs From Climate Change? – Amelia Urry – NewsDeeply

Study: Several important vaginal metabolites elevated in smokers – Bob Kronemyer – Modern Medicine

Doctors collect viruses from pond and employ them to combat a man’s antibiotic resistance infection in man’s heart – Mark Kaufman – Mashable

Making good bacteria more resilient – Gali Weinreb – Globes

Study links decline of ‘good’ bacteria in infants to higher long-term increases in pH of poo – Tim Cutcliffe – NUTRAingredients

Microbes on the market

German biotech company wants to turn old PCs into gold – Jeremy Gray – Handelsblatt Global – European Business & Finance News

 

March 11, 2018

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Events and jobs

EVEN seminar: Weakest link in water quality control: Drinking water biofilm in premise plumbing – INSTAAR, CU Boulder

General microbiome

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes – Aura Ferreiro, Cell

Egalitarianism in Biofilms – Dawen Gao, Microbial Ecology

Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds – Hui Wang, Frontiers in Microbiology

Human multi-site microbiome

The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis – Raphaël Enaud, Microorganisms

Human gut microbiome

Gut Microbiota Alteration After Long-Term Consumption of Probiotics in the Elderly – Renyuan Gao, Probiotics and Antimicrobial Proteins

Sex differences in gut microbiota in patients with major depressive disorder – Chen JJ, Neuropsychiatric Disease and Treatment

Oral microbiome

Influence of periodontal treatment on subgingival and salivary microbiotas – Daniel Belstrøm, Journal of Periodontology

Microbiome at sites of gingival recession in children with Hutchinson–Gilford progeria syndrome – Seyed Hossein Bassir, Journal of Periodontology

Subgingival microbial profile of obese women with periodontal disease – Carina M. Silva-Boghossian, Journal of Periodontology

Animal experiments

The effect of probiotics and polysaccharides on the gut microbiota composition and function of weaned rats – Mengxia Wang, Food and Function

Cecal Versus Fecal Microbiota in Ossabaw Swine and Implications for Obesity – Matthew R Panasevich, Physiological Genomics

Antibiotics-induced modulation of large intestinal microbiota altered aromatic amino acid profile and expression of neurotransmitters in the hypothalamus of piglets – Kan Gao, Journal of Neurochemistry

Animal microbiome

Nutrient factories: Metabolic function of beneficial microorganisms associated with insects – Nana Y. D. Ankrah, Environmental Microbiology

Community composition, diversity, and metabolism of intestinal microbiota in cultivated European eel (Anguilla anguilla) – Wei Huang, Applied Microbiology and Biotechnology

Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs – Brandon J. Varela, Frontiers in Microbiology

Influence of Novel Highly Pathogenic Avian Influenza A (H5N1) Virus Infection on Migrating Whooper Swans Fecal Microbiota – Na Zhao, Frontiers in Cellular and Infectious Microbiology

Plant, root, and soil microbiome

The Soil-Borne Legacy – Peter A.H.M. Bakker, Cell

Water and extremophile microbiome

Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic – Omar Federico Ordoñez, Microbial Ecology

Occurrence of Legionella in Nonpotable Reclaimed Water – William J. Johnson, American Water Works Association

Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi’an, China – Haihan Zhang, International Journal of Environmental Research and Public Health

Food microbiome

Microbial community and physicochemical dynamics during the production of ‘Chicha’, a traditional beverage of Indigenous people of Brazil – Ludmila Vilela Resende, World Journal of Microbiology and Biotechnology

Techniques

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton – Emma K. Wear, Environmental Microbiology

Microbes in the news

Pitting Viruses Against Bacteria To Combat The Antibiotic Crisis – SciFri

March 10, 2018

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Many interesting perspectives from a recent mSystems issue, along with plenty of plant/soil articles!

Events and jobs
Group Leader R&D | (Microbiology/Biomarkers), 8685 – Stratacuity: Proven Scientific Placement  Company – Boston, Massachusetts

General microbiome
Preprint: Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – bioRxiv

Preprint/Review: Host genetics and microbiome associations from the lens of genome wide association studies – Omer Weissbrod – PeerJ

Review: Studying microbial functionality within the gut ecosystem by systems biology – Bastian Hornung – BMC Genes and Nutrition

Perspective: Making Millennial Medicine More Meta – Peter J. Turnbaugh – MSystems

Perspective: Spatial Analyses of Specialized Metabolites: The Key to Studying Function in Hosts – Melissa M. Galey – MSystems

Pregnancy and early life
Development of the Human Mycobiome over the First Month of Life and across Body Sites – Tonya L. Ward – mSystems

The potential of gut microbiota and fecal volatile organic compounds analysis as early diagnostic biomarker for necrotizing enterocolitis and sepsis in preterm infants – Daniel Johannes Cornelis Berkhout – Expert Review of Gastroenterology & Hepatology

Review: Factors Affecting the Immunity to Respiratory Syncytial Virus: From Epigenetics to Microbiome. – Wendy Fonseca – Frontiers In Immunology

Human respiratory microbiome
The Nasal Microbiome in Asthma. – Mina Fazlollahi – The Journal Of Allergy And Clinical Immunology

Human oral microbiome
Review: Metatranscriptome of the Oral Microbiome in Health and Disease. – J Solbiati – Journal Of Dental Research

Human vaginal microbiome
The effect of vaginal microbial communities on colonization by Staphylococcus aureus with the gene for toxic shock syndrome toxin 1 (TSST-1): a case control study – Jacob D Pierson – Pathogens and Disease

Human gut microbiome
Preprint: Gut microbiota density influences host physiology and is shaped by host and microbial factors – Eduardo Contijoch – bioRxiv

Review: Gender Differences in the Gut Microbiome and How These Affect Cardiovascular Diseases – Adriana Cabal – Gender Differences in the Pathogenesis and Management of Heart Disease

Microbial ecology
Perspective: A Microbial Perspective on the Grand Challenges in Comparative Animal Physiology – Kevin D. Kohl – mSystems

Animal experiments
Rapid environmental effects on gut nematode susceptibility in rewilded mice. – Jacqueline M Leung – Plos Biology

Calcineurin B in CD4+ T Cells Prevents Autoimmune Colitis by Negatively Regulating the JAK/STAT Pathway – Andrea Mencarelli – Frontiers In Immunology

Green tea extract and black tea extract differentially influence cecal levels of short-chain fatty acids in rats – Tomonori Unno – Food Science and Nutrition

Animal microbiome
Detailed ecological associations of triatomines revealed by metabarcoding and next-generation sequencing: implications for triatomine behavior and Trypanosoma cruzi transmission cycles. – Eric Dumonteil – Scientific Reports

Comparative Metagenomic Profiling of Viromes Associated with Four Common Mosquito Species in China – Han Xia – Virologica Sinica

Preprint: Two novel strains of Torulaspora delbrueckii isolated from the honey bee microbiome and their use in honey fermentation – Joseph P. Barry – bioRxiv

16S rRNA metagenomic analysis of the symbiotic community structures of bacteria in foregut, midgut, and hindgut of the wood-feeding termite Bulbitermes sp. – Yue Ming Chew – Symbiosis

Plant, root, and soil microbiome
Towards a Natural History of Soil Bacterial Communities – Jennifer B.H. Martiny – Trends in Microbiology

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. – Binu M Tripathi – The Isme Journal

Composition of bacterial community in enrichment cultures of shale by-products from Irati Formation, Brazil – Kelly Campos Guerra Pinheiro de Goes – Brazilian Journal of Microbiology

Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity – Ulas Karaoz – mBio

Long-term irrigation affects the dynamics and activity of the wheat rhizosphere microbiome – Dmitri Mavrodi – Frontiers in Plant Science

Specialized core bacteria associate with plants adapted to adverse environment with high calcium contents. – Fei Li – Plos One

Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum – Meng Dong – Frontiers In Microbiology

Long-Term Harvest Residue Retention Could Decrease Soil Bacterial Diversities Probably Due to Favouring Oligotrophic Lineages – Yaling Zhang – Microbial Ecology

Trichoderma-Inoculated Miscanthus Straw Can Replace Peat in Strawberry Cultivation, with Beneficial Effects on Disease Control – Jane Debode – Frontiers In Plant Science

Heterologous Expression of Secreted Bacterial BPP and HAP Phytases in Plants Stimulates – Lia R Valeeva – Frontiers In Plant Science

Perspective: Metabolomics and Agriculture: What Can Be Done? – Rodolpho Martin do Prado – MSystems

Perspective: Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology – Marnix H. Medema – mSystems

Soil Inoculation with Bacillus spp. Modifies Root Endophytic Bacterial Diversity, Evenness, and Community Composition in a Context-Specific Manner – Kiran R. Gadhave – Microbial Ecology

Book: Advances in Soil Microbiology: Recent Trends and Future Prospects – Tapan Kumar Adhya:
Many chapters may be of interest, including:

Water and extremophile microbiome
Persistent nitrogen limitation of stream biofilm communities along climate gradients in the arctic. – Maria Myrstener – Global Change Biology

Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding – Rippin Martin – FEMS Microbiology Ecology

Archaeal community compositions in tilapia pond systems and their influencing factors – Limin Fan – World Journal of Microbiology and Biotechnology

Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics. – Rafael R C Cuadrat – Frontiers In Microbiology

Abundance and observations of thermophilic microbial and viral communities in submarine and terrestrial hot fluid systems of the French Southern and Antarctic Lands – Kaarle J. Parikka – Polar Biology

An Assessment of Sub-Meter Scale Spatial Variability of Arcellinida (Testate Lobose Amoebae) Assemblages in a Temperate Lake: Implications for Limnological Studies – Riley E. Steele – Microbial Ecology

Built environment
The classroom microbiome and asthma morbidity in children attending three inner-city schools. – Peggy S Lai – The Journal Of Allergy And Clinical Immunology

Decomposition of lignocellulose and readily degradable carbohydrates during sewage sludge biodrying, insights of the potential role of microorganisms from a metagenomic analysis – Lu Cai – Chemosphere

Illumina MiSeq Sequencing reveals microbial community in HA process for dyeing wastewater treatment fed with different co-substrates – Xuehui Xie – Chemosphere

Food microbiology
An Ultrahigh-Performance Liquid Chromatography-Time-of-Flight Mass Spectrometry Metabolomic Approach to Studying the Impact of Moderate Red-Wine Consumption on Urinary Metabolome – Adelaida Esteban-Fernández – Journal of Proteome Research

Probiotics / prebiotics / antibiotics
Fate of antibiotic and metal resistance genes during two-phase anaerobic digestion of residue sludge revealed by metagenomic approach. – V Richarte – Environmental Science And Pollution Research International

Intra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential. – Jason W Arnold – Frontiers In Microbiology

Phages and viruses
Deciphering the Human Virome with Single-Virus Genomics and Metagenomics – Maria José de la Cruz Peña – Viruses

Urinary Virome perturbations in kidney transplantation – Neil Mercer – Frontiers in Microbiology

Preprint: Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity – Mariann Landsberger – bioRxiv

Preprint: Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity – Adair L Borges – bioRxiv

Bioinformatics
From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool – Simone Rampelli – Viral Metagenomics

Techniques
Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion. – Diane Plouchart – Plos One

Review: Electrochemical Probes of Microbial Community Behavior – Hunter J. Sismaet – Annual Review of Analytical Chemistry

Antibiotic-Responsive Bioart: Exploring DIYbio as a Design Studio Practice – Stacey Kuznetsov – ACM

Microbes in the news
Four stories of antibacterial breakthroughs – Natasha Gilbert – Nature

How baby’s first microbes could be crucial to future health – Sarah DeWeerdt – Nature

Hacking a Cow’s Gut Bacteria Could Make More Meat, Less Pollution – Chelsea Gohd – Futurism

High-Fiber Diet Shifts Gut Microbes, Lowering Blood Sugar in Diabetics – Ashley Yeager – The Scientist

March 9, 2018

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Have a nice Friday! Today we have interesting papers about nasal/oral microbiota, some papers about studies in pathogens (including the use of bacteriophages for selective inhibition of E. coli), DNA extraction studies in meconium, and more!

 

Human/General Microbiome

Review: Microbiota metabolites: Pivotal players of cardiovascular damage in chronic kidney disease – Carmela Cosola – Pharmacological Research

Predictive biomarkers for type 2 of diabetes mellitus: bridging the gap between systems research and personalized medicine – Christina Kraniotou – Journal of Proteomics

The Nasal Microbiome in Asthma – Mina Fazlollahi – Journal of Allergy and Clinical Immunology

Metatranscriptome of the Oral Microbiome in Health and Disease – J. Solbiati – Journal of Dental Research

Nasal Microbiota and Respiratory Tract Infections: The Role of Viral Detection – Insa Korten – American Journal of Respiratory and Critical Care Medicine

Short term dynamics of the sputum microbiome among COPD patients – Rohita Sinha – Plos One

The effect of medical treatments on the bacterial microbiome in patients with chronic rhinosinusitis: a pilot study – Ravi Jain – International Forum of Allergy & Rhinology

The Influence of Cervicovaginal Microbiota on Mucosal Immunity and Prophylaxis in the Battle against HIV – Mara Farcasanu – Current HIV/AIDS Reports

Emerging Mechanisms of Innate Immunity and Their Translational Potential in Inflammatory Bowel Disease – Daniele Corridoni – Frontiers in Medicine

Oropharyngeal Microbiota in Frail Older Patients Unaffected by Time in Hospital – Victoria C. Ewan – Frontiers In Cellular And Infection Microbiology

Influence of Intestinal Indigenous Microbiota on Intrafamilial Infection by Helicobacter pylori in Japan – Takako Osaki – Frontiers in Immunology

Comparison of Meconium DNA Extraction Methods for Use in Microbiome Studies – Lisa F. Stinson – Frontiers in Microbiology

Minireview: Gut Microbiota: An Integral Moderator in Health and Disease – Qingqing Feng –   Frontiers in Microbiology

Activation of Notch-1 in oral epithelial cells by P. gingivalis triggers the expression of the antimicrobial protein PLA2-IIA – Ahmad Al-Attar – Mucosal Immunology

Gut microbial RNA and DNA analysis predicts hospitalizations in cirrhosis – Jasmohan S. Bajaj –  JCI Insight

Physiological Regulation of Drug Metabolism and Transport: Pregnancy, Microbiome, Inflammation, Infection, and Fasting – Edward T. Morgan – Drug Metabolism and Disposition

 

Pathogen Research

A bacteriophage cocktail targeting Escherichia coli reduces E. coli in simulated gut conditions, while preserving a non-targeted representative commensal normal microbiota – Tomasz Cieplak – Gut Microbes

Triclosan Enhances the Clearing of Pathogenic Intracellular Salmonella or Candida albicans but Disturbs the Intestinal Microbiota through mTOR-Independent Autophagy – Chao Wang – Frontiers In Cellular And Infection Microbiology

The Metabolic Sensor GPR43 Receptor Plays a Role in the Control of Klebsiella pneumoniae Infection in the Lung – Izabela Galvão – Frontiers in Immunology

Parasite-Vector Interaction of Chagas Disease: A Mini-Review – Ana Beatriz Bortolozo de Oliveira – The American Journal of Tropical Medicine and Hygiene – Current Issue

Bacillus subtilis spore with surface display of paramyosin from Clonorchis sinensis potentializes a promising oral vaccine candidate – Hengchang Sun – Parasites & Vectors

 

Animal Microbiome

Instar- and host-associated differentiation of bacterial communities in the Mediterranean fruit fly Ceratitis capitata – Antonino Malacrinò – Plos One

Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates – Tasha Barr – Gut Microbes

Integrating molecular and ecological approaches to identify potential polymicrobial pathogens over a shrimp disease progression – Wenfang Dai – Applied Microbiology And Biotechnology

Intestinal bacterial signatures of white feces syndrome in shrimp – Dongwei Hou – Applied Microbiology And Biotechnology

Bile acid metabolism regulated by the gut microbiota promotes non-alcoholic steatohepatitis-associated hepatocellular carcinoma in mice – Shoji Yamada – Oncotarget

Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila – Fumiaki Obata – Nature Communications

Physiological mechanisms of sustained fumagillin-induced weight loss – Jie An – JCI Insight

Gpr109a Limits Microbiota-Induced IL-23 Production To Constrain ILC3-Mediated Colonic Inflammation – Brinda Bhatt – The Journal in Immunology

Fuzhuan brick tea polysaccharides attenuate metabolic syndrome in high-fat diet induced mice in association with modulation in the gut microbiota – Guijie Chen – Journal Of Agricultural And Food Chemistry

 

Extremophiles

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) – Blanca Vera-Gargallo – Genes

 

Plant Microbiome

Disease-induced assemblage of a plant-beneficial bacterial consortium – Roeland L. Berendsen – The ISME Journal