April 11, 2018

In today’s digest, check among many interesting articles: the evolution within human microbiome by T.D. Lieberman,  unique microbial biodiversity residing in hadal trenches by L.M. Peoples, changes in community composition in coastal water following exposure to oil and oil dispersant by S.H. Doyle. While in news — a story about “microbial hitchhikers” in restroom hand dryers.

General microbiome

Seven Billion Microcosms: Evolution within Human Microbiomes – Tami D. Lieberman – mSystems

Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead – Benjamin E. Wolfe – mSystems

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

Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation –  Hyaekang Kim – PLOS One

New insight into the early stages of biofilm formation – Catherine R. Armbruster  – PNAS

Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation – Jeronimo Rodriguez-Beltran – Nature Ecology & Evolution

Considering the Lives of Microbes in Microbial Communities – Elizabeth A. Shank – mSystems

Oral microbiome

Inflammatory Bacteriome and Oral Squamous Cell Carcinoma – M. Perera – Journal of Dental Research

Human gut microbiome

The cardiovascular macrophage: a missing link between gut microbiota and cardiovascular diseases? – X. Chen – European Review for Medical and Pharmacological Sciences

Can Diet Influence Our Health by Altering Intestinal Microbiota – Derived Fecal Metabolites? – Qiang Lyu – mSystems

Toward Personalized Control of Human Gut Bacterial Communities – Lawrence A. David – mSystems

Role of the Gut Microbiome in Vertebrate Evolution – Thomas J. Sharpton – mSystems

Dietary nutrition and gut microflora: A promising target for treating diseases – Ying Nie – Trends in Food Science & Technology

Reduction in hepatic secondary bile acids caused by short-term antibiotic-induced dysbiosis decreases mouse serum glucose and triglyceride levels – Takuya Kuno – Scientific Reports

A snapshot of gut microbiota of an adult urban population from Western region of India – Disha Tandon – PLOS One

Animal experiments 

Mice harboring pathobiont-free microbiota do not develop intestinal inflammation that normally results from an innate immune deficiency – Benoit Chassaing – PLOS One

Animal microbiome 

The cultivable autochthonous microbiota of the critically endangered Northern bald ibis (Geronticus eremita) – Joachim Spergser – PLOS One

Plant, root, and soil microbiome

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth – Heather C. Manching –  F1000 Research

Exploring the Potentiality of Novel Rhizospheric Bacterial Strains against the Rice Blast Fungus Magnaporthe oryzae – Narayanappa Amruta –  The Plant Pathology Journal

The sensitivity of soil enzymes, microorganisms and spring wheat to soil contamination with carfentrazone-ethyl – Monika Tomkiel – Journal of Environmental Science and Health, Part B

Water and extremophile microbiome 

Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea, northern China – Mamun Abdullah Al – European Journal of Protistology

Vertically distinct microbial communities in the Mariana and Kermadec trenches – Logan M. Peoples – PLOS One

The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum – Tianyong Zheng – PLOS One

Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy – Shawn E. McGlynn – Applied and Environmental Microbiology

Addressing Confounding Factors in Algal Phosphorus Limitation Experiments – Whitney S. Beck -bioRxiv

Effect of Siderophore on Iron Availability in a Diatom and a Dinoflagellate Species: Contrasting Response in Associated Bacteria – Nicolas Sanchez – Frontiers in Marine Science

Robust Mercury Methylation across Diverse Methanogenic Archaea – Cynthia C. Gilmour – mBio

Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris – Anthony R. Miller – mBio

Trichodesmium physiological ecology and phosphate reduction in the western Tropical South Pacific – Kyle R. Frischkorn – Biogeosciences

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea – Michael F. Graw- Frontiers in Microbiology

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit – Shawn M. Doyle – Frontiers in Microbiology

Understanding Diatom Cell Wall Silicification—Moving Forward – Mark Hildebrand – Frontiers in Marine Science

The hunt for the most-wanted chemolithoautotrophic spookmicrobes – Michiel H in ‘t Zandt – FEMS Microbiology Ecology

Biotechnology

Electron transport chains in organohalide-respiring bacteria and bioremediation implications – Shanquan Wang – Biotechnology Advances

Food microbiology

Listeria monocytogenes strains show large variations in competitive growth in mixed culture biofilms and suspensions with bacteria from food processing environments – Even Heir – International Journal of Food Microbiology

Review: Titanium dioxide (TiO2) photocatalysis technology for nonthermal inactivation of microorganisms in foods – Zhiwei Zhu – Trends in Food Science & Technology

The complexity of wine: clarifying the role of microorganisms – Sophie Tempère – Applied Microbiology and Biotechnology

Probiotics / prebiotics

The effect of Lactobacillus acidophilus and Lactobacillus casei on the in vitro bioaccessibility of flaxseed lignans (Linum usitatissimum L.) – O. Muñoz – Food & Function

The “Golden Age” of Probiotics: A Systematic Review and Meta-Analysis of Randomized and Observational Studies in Preterm Infants – Dermyshi E. – Neonatology

Phages and viruses

Screening of FDA-approved Drugs and Identification of Novel Lassa Virus Entry Inhibitors – Peilin Wang – bioRxiv

Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater – Nichole E. Brinkman – PLOS One

Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus – Piotr M. Skowron – PLOS One

Bioinformatics

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data – Li Chen – PeerJ

Techniques

Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae – Matthew A. Croxen –  Microbial Genomics

Paraffin Embedding and Thin Sectioning of Microbial Colony Biofilms for Microscopic Analysis – William C. Cornell – Journal of Visualized Experiments (Jove)

Microbes in the news 

Bugs, microbes and death can inform the living

Gut bacteria keeps bears healthily obese

Restroom Hand Dryers Are Blowing Bacteria Everywhere

Survival strategy: How one enzyme helps bacteria recover from exposure to antibiotics

Oil-eating bacteria could clean up the next spill

 

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March 28, 2018

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 18, 2018

An interesting book and multiple animal microbiome papers for today’s digest!

General microbiome
Book: Clinical Immunology (Fifth Edition): Principles and Practice – Robert R. Rich, Thomas A. Fleisher, William T. Shearer, Harry W. Schroeder, Anthony J. Frew, Cornelia M. Weyand
Multiple chapters may be of interest, including:

Human skin microbiome
Review: Cutaneous Barriers and Skin Immunity: Differentiating A Connected Network – Stefanie Eyerich – Trends in Immunology

Human gut microbiome
TonB-dependent transport by the gut microbiota: novel aspects of an old problem – David N Bolam – Current Opinion on Structural Biology

ReviewFrailty and the gut – Antonio Di Sabatino – Digestive and Liver Disease

Animal experiments
Chronic exposure to low concentrations of lead induces metabolic disorder and dysbiosis of the gut microbiota in mice – Jizhou Xia – Science of the Total Environment

Polystyrene microplastics induce gut microbiota dysbiosis and hepatic lipid metabolism disorder in mice – Liang Lu – Science of the Total Environment

Expression of recombinant human lysozyme in bacterial artificial chromosome transgenic mice promotes the growth of Bifidobacterium and inhibits the growth of Salmonella in the intestine – Lu Dan – Journal of Biotechnology

Comparative analysis of gut microbial community in healthy and tibial dyschondroplasia affected chickens by high throughput sequencing – Xiaole Tong – Microbial Pathogenesis

Polysaccharide of Hericium erinaceus Attenuates Colitis in C57BL/6 Mice via Regulation of Oxidative Stress, Inflammation-related Signaling Pathways and Modulating the Composition of the Gut Microbiota – Yilin Ren – The Journal of Nutritional Biochemistry

Variations in methane yield and microbial community profiles in the rumen of dairy cows as they pass through stages of first lactation – Tamsin Lyons – Journal of Dairy Science

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

Microbiomes associated with bovine periodontitis and oral health – Ana C. Borsanelli – Veterinary Microbiology

ReviewCurrent perspectives of the chicken gastrointestinal tract and its microbiome – D. Borda-Molina – Computational and Structural Biotechnology Journal

Built environment
Review: Bioremediation of a pentacyclic PAH, Dibenz(a,h)Anthracene- A long road to trip with bacteria, fungi, autotrophic eukaryotes and surprises – Vidya Vasudevan – Chemosphere

Food microbiology
Microbial community dynamics of a blue-veined raw milk cheese from the United Kingdom – Dewi Yunita – Journal of Dairy Science

Probiotics / prebiotics / antibiotics
A mathematical model of multiple delayed feedback control system of the gut microbiota—Antibiotics injection controlled by measured metagenomic data – Yueping Dong – Nonlinear Analysis: Real World Applications

Review: Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics – Zachary JS Mays – Current Opinion in Biotechnology

ReviewThe role of the gut microbiota in the pathology and prevention of liver disease – Alejandra Altamirano-Barrera – The Journal of Nutritional Biochemistry

Phages and viruses
Preprint: Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem – Divya Venkatesh – bioRxiv

New Genomes
Sanguibacter massiliensis sp. nov., Actinomyces minihominissp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov., and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples. – Melhem Bilen – New Microbes and New Infections

Microbes in the news
Weighty challenge: Untangling obesity’s hidden picture – Jamie Morton – NZ Herald

Microbes on the market
Seres Therapeutics (NASDAQ:MCRB) Upgraded at Zacks Investment Research – Amber Thompson – Register Journal

March 15, 2018

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 13, 2018

In today’s digest it was quite hard to pick just few papers, since there are many, many interesting papers. From mentioned reviews I would recommend the one by H. Bokhari on the exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens and the one by J. R. Bober on engineering probiotics and microbes for biomedical applications. From other papers I would like to highlight the one by M. Mehrshad and enigmatic SAR202 cluster, the one by A. C. Lehours and biogeographic patterns of aerobic anoxygenic phototrophic bacteria and the one by E. M. Llufrio and how fluorescence activated cell sorting introduces oxidative stress and alters the metabolic state of cells. Don’t forget to check on news, where you can read about metagenomic clustering powered by supercomputers, while in general science section there is an interesting article by B. Barros on ‘scientific knowledge percolation process’ or how scientific information diffuse into the social sphere.

General microbiome

Review: Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens – Habib Bokhari – Critical Reviews in Microbiology

The aryl hydrocarbon receptor as a moderator of host-microbiota communication – Limin Zhang – Current Opinion in Toxicology

Pregnancy and early life

The Role of the Microbiome in the Developmental Origins of Health and Disease – Leah T. Stiemsma – Pediatrics

Human gut microbiome

 

Translocation of a gut pathobiont drives autoimmunity in mice and humans – S. Manfredo Vieira – Science

Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome – Laura-Isobel McCall – PLOS One

How to Increase the Butyrate-Producing Capacity of the Gut Microbiome: Do IBD Patients Really Need Butyrate Replacement and Butyrogenic Therapy? – Stanislav Sitkin – Journal of Crohn’s and Colitis

Effect of Faecal Microbiota Transplantation for Treatment of Clostridium difficile Infection in Patients with Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis of Cohort Studies – Tuo chen –  Journal of Crohn’s and Colitis

Animal experiments 

Supplementation of Bacillus subtilis based probiotic reduces heat stress-related behaviors and inflammatory response in broiler chickens – W C Wang – Journal of Animal Science

Comparisons of bacterial and Archaeal Communities in the Rumen and a Dual-Flow Continuous Culture Fermentation System using Amplicon Sequencing – I J Salfer – Journal of Animal Science

The Microbiome Regulates Pulmonary Responses to Ozone in Mice – Youngji Cho – American Journal of Respiratory Cell and Molecular Biology

Bifidobacteria exert species-specific effects on constipation in BALB/c mice – Linlin Wang – Food & Function

Animal microbiome 

Comparative Analysis of the Gut Bacterial Community of Four Anastrepha Fruit Flies (Diptera: Tephritidae) Based on Pyrosequencing – Carmen Ventura – Current Microbiology

Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats’ rumen – Thi Huyen Do – The Journal of General and Applied Microbiology

Plant, root, and soil microbiome

Colonization of Eggplant by Endophytic Bacteria Antagonistic to Ralstonia solanacearum, the Bacterial Wilt Pathogen – Gauri A. Achari – Proceedings of the National Academy of Sciences, India Section B: Biological Sciences

Landscape scale factors affecting prevalence of Escherichia coli in surface soil include land cover type, edge interactions, and soil pH – Nicholas Dusek – Applied and Environmental Microbiology

Nigericin and grisorixin methyl ester from the Algerian soil-living Streptomyces youssoufiensis SF10 strain: a computational study on their epimeric structures and evaluation of glioblastoma stem cells growth inhibition – Nassima Leulmi – Natural Product Research

Interacting effect of diclofop-methyl on the rice rhizosphere microbiome and denitrification – Haifeng Qian – Pesticide Biochemistry and Physiology

Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes – Carmen Gómez-Lama Cabanás  – Frontiers in Microbiology

Resveratrol as a growth substrate for bacteria from the rhizosphere – Zohre Kurt – Applied and Environmental Microbiology

Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits – Jonathan W. Leff – The ISME Journal

Diversity of microbial communities potentially involved in mercury methylation in rice paddies surrounding typical mercury mining areas in China – Xin Liu – Microbiology Open

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses – Michael Hemkemeyer – Frontiers in Microbiology

Volatile compounds from beneficial or pathogenic bacteria differentially regulate root exudation, transcription of iron transporters, and defense signaling pathways in Sorghum bicolor – Erasto Hernández-Calderón –  Plant Molecular Biology

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C. A. Mallon – The ISME Journal

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root–rhizosphere interactome – Etienne Yergeau – The ISME Journal

Bioaugmentation of chlorothalonil-contaminated soil with hydrolytically or reductively dehalogenating strain and its effect on soil microbial community – Xi-Hui Xu – Journal of Hazardous Materials

Water and extremophile microbiome 

Biogeographic patterns of aerobic anoxygenic phototrophic bacteria reveal an ecological consistency of phylogenetic clades in different oceanic biomes – Anne-Catherine Lehours – Scientific Report

Mercury-methylating bacteria are associated with zooplankton: a proof-of-principle survey in the Baltic Sea –  Elena Gorokhova – bioRxiv

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

Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows – Songlin Liu – Microbiology Open

Chapter 17 – Rhizosphere Metabolite Profiling: An Opportunity to Understand Plant-Microbe Interactions for Crop Improvement -Amit Verma – Crop Improvement Through Microbial Biotechnology

Chapter 22 – Plant-Microbe Interaction and Genome Sequencing: An Evolutionary Insight – Krishna K. Sharma – Crop Improvement Through Microbial Biotechnology

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

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management – Domenico Savio – Wiley Interdisciplinary Reviews: Water

Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments – Kathleen M. Scott – Environmental Microbiology

Data Article: Bioinformatics delimitation based on sequence data of the psychrophilic and psychrotolerant actinobacteria isolated from the Polar Frontal waters of the Antarctic Ocean – Palaniappan Sivasankar – Data in Brief

Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity – Kai Tang – Frontiers in Microbiology

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling – Maliheh Mehrshad – The ISME Journal

The widespread dissemination of integrons throughout bacterial communities in a riverine system – Gregory C. A. Amos – The ISME Journal

Expression profiling of host and virus during a coccolithophore bloom provides insights into the role of viral infection in promoting carbon export – Uri Sheyn – The ISME Journal

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations – Sarahi L. Garcia – The ISME Journal

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota – Lin-Xing Chen – The ISME Journal

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases – Andrea G. Bravo – The ISME Journal

Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef  – Michael P. Lesser – The ISME Journal

Multiple colonist pools shape fiddler crab-associated bacterial communities – Catalina Cuellar-Gempeler – The ISME Journal

Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. – Mikhail A. Moldovan – Frontiers in Microbiology

Halotolerant Exiguobacterium profundum PHM11 Tolerate Salinity by Accumulating L-Proline and Fine-Tuning Gene Expression Profiles of Related Metabolic Pathways – Vikas K. Patel – Frontiers in Microbiology

The predictability of a lake phytoplankton community, over time-scales of hours to years – Mridul K. Thomas – Ecology Letters

Built environment

Anaerobic Ammonium-Oxidizing Bacteria in Cow Manure Composting – Tingting Wang – Journal of Microbiology and Biotechnology

Petrophilic, Fe(III) Reducing Exoelectrogen Citrobacter sp. KVM11, Isolated From Hydrocarbon Fed Microbial Electrochemical Remediation Systems – Krishnaveni Venkidusamy – Frontiers in Microbiology

Inhibitors degradation and microbial response during continuous anaerobic conversion of hydrothermal liquefaction wastewater – Buchun Sia – Science of The Total Environment

Food microbiology

Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation – Francesca De Filippis – Food Microbiology

Staphylococcus aureus undergoes major transcriptional reorganization during growth with Enterococcus faecalis in milk – Gabriela NogueiraViçosa – Food Microbiology

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts – Food Microbiology

Changes in microbial communities and quality attributes of white muscle and dark muscle from common carp (Cyprinus carpio) during chilled and freeze-chilled storage – Qian Li – Food Microbiology

Microbial diversity and chemical analysis of the starters used in traditional Chinese sweet rice wine – Haiying Cai –  Food Microbiology

Structure of association networks in food bacterial communities – Eugenio Parente – Food Microbiology

Shifts in spinach microbial communities after chlorine washing and storage at compliant and abusive temperatures – Ganyu Gu – Food Microbiology

Probiotics / prebiotics

Effective identification of Lactobacillus casei group species: genome-based selection of the gene mutL as the target of a novel multiplex PCR assay – Benedetta Bottari – Microbiology

Phages and viruses

A Holistic Assessment of the Risks and Benefits of the Synthesis of Horsepox Virus – Diane Di Euliis – mSphere

Biotechnology

Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting – Caihong Song – Bioresource Technology

Review: Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications – Josef R. Bober – Annual Review of Biomedical Engineering

Techniques

Sorting Cells Alters Their Redox State and Cellular Metabolome – Elizabeth M. Llufrio – Redox Biology

Microbes in the news 

Ibuprofen Counters Key Bacteria in Lungs of CF Patients, Study Shows

Bacteria in your intestines can trigger autoimmune diseases

A game changer: Metagenomic clustering powered by supercomputers

Science, publishing, and career

Scientific knowledge percolation process and social impact: a case study on the biotechnology and microbiology perceptions on Twitter – Beatriz Barros – Science and Public Policy

March 11, 2018

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 3, 2017

Antiphage defense systems in microbial genomes, oral pathogen inhibition by wine polyphenols and an oral probiotic, and analysis of E. coli gene expression in simulated spaceflight.

Events and jobs

Call for Expressions of Interest: Microbiology Twitter Teachers for New MOOC – Spanish Society for Microbiology

Endowed Chair in Molecular Genetics Waksman Institute of Microbiology – Rutgers University

General microbiome

Creating a 3D microbial and chemical snapshot of a human habitat – Clifford A Kapono – Scientific Reports

Human oral microbiome

Inhibition of Oral Pathogens Adhesion to Human Gingival Fibroblasts by Wine Polyphenols Alone and in Combination with an Oral Probiotic – Adelaida Esteban-Fernández – Journal of Agricultural and Food Chemistry

Human vaginal microbiome

Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Zhi-Luo Deng – bioRxiv

Human gut microbiome

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A Rosa – Microbiome

Animal experiments

Pre-print: Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal – Sean M Kearney – bioRxiv

Pre-print: Clearing the FoG: Antifungal tolerance is a subpopulation effect that is distinct from resistance and is associated with persistent candidemia – Alexander Rosenberg – bioRxiv

Blueberry Supplementation Influences the Gut Microbiota, Inflammation, and Insulin Resistance in High-Fat-Diet–Fed Rats – Sunhye Lee – Journal of Nutrition

Animal microbiome

Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus – Biao Chen – AMB Express

Water and extremophile microbiome

Pre-print: Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom – Rasmus Swalethorp – bioRxiv

Microbes in space

Pre-print: Analysis of Escherichia coli Flagellin Gene Expression in Simulated Spaceflight Growth Conditions – Kyle M Hetrick – bioRxiv

Phages and viruses

Systematic discovery of antiphage defense systems in the microbial pangenome – Shany Doron – Science

Bioinformatics

Pre-print: VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma – Atlas Khan – bioRxiv

Techniques

Pre-print: Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets – Edouard A Hay – bioRxiv

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem – Stilianos Louca – Microbiome

Improving saliva shotgun metagenomics by chemical host DNA depletion – Clarisse A Marotz – Microbiome

Microbes in the news

Your skin is crawling with bacteria, and some of them might help fight cancer – Claire Maldarelli – Popular Science

Most Viruses And Bacteria Fall From The Sky – Astrobiology Web

Microbes on the market

Six Leading Pharma Firms to Participate at Pharmaceutical Microbiology Event in San Diego – Technology Networks

Science, career, and publishing

Pre-print: Persistent Underrepresentation of Women’s Science in High Profile Journals – Yiqin Alicia Shen – bioRxiv

Pre-print: Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist – Holly O Witteman – bioRxiv