Category Archives: Human gut

April 13, 2017

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Profiles of ulcerative colitis patients’ microbiota after fecal microbiota transplantation, a bioinformatics software package for rarefaction analysis, an artist who uses sweat and bacteria to create scents and sculptures.

General microbiome

Review: Microbial metabolites in nutrition, healthcare and agriculture – Rajendra Singh – 3 Biotech

Review: Modified Mediterranean Diet for Enrichment of Short Chain Fatty Acids: Potential Adjunctive Therapeutic to Target Immune and Metabolic Dysfunction in Schizophrenia? – Jamie Joseph – Frontiers in Neuroscience

Human respiratory microbiome

The Nasopharyngeal Microbiota of Children with Respiratory Infections in Botswana – Matthew S Kelly – Pediatric Infectious Disease Journal

Human gut microbiome

* Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation – Susana Fuentes – ISME Journal

Intestinal microbiome in children with severe and complicated acute viral gastroenteritis – Shih-Yen Chen – Scientific Reports

Unusual active site location and catalytic apparatus in a glycoside hydrolase family – Jose Munoz-Munoz – PNAS

Animal experiments

Enterococcus faecalis bacteriocin EntV inhibits hyphal morphogenesis, biofilm formation, and virulence of Candida albicans – Carrie E Graham – PNAS

The therapeutic protection of a living and dead Lactobacillus strain against aluminum-induced brain and liver injuries in C57BL/6 mice – Fengwei Tian & Leilei Yu – PLOS One

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria – Yusuke Nagara – PLOS One

Review: Caspase recruitment domain 9, microbiota, and tryptophan metabolism: dangerous liaisons in inflammatory bowel diseases – Bruno Lamas – Current Opinion in Clinical Nutrition and Metabolic Care

Individual variation of natural D. melanogaster associated bacterial communities – Yun Wang – bioRxiv

Plant, root, and soil microbiome

A new polyketide glycoside from the rhizospheric Clonostachys rogersoniana associated with Panax notoginseng – Tian-Peng Yin – Journal of Asian Natural Products Research

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter – Ember M Morrissey – ISME Journal

Population and function analysis of cultivable bacteria associated with spores of arbuscular mycorrhizal fungus Gigaspora margarita – Liangkun Long – 3 Biotech

Water and extremophile microbiome

Exploring the ecological coherence between the spatial and temporal patterns of bacterioplankton in boreal lakes – Juan P. Niño García – Frontiers in Microbiology

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems – Sean P Jungbluth – PeerJ

Bacterial community composition and dynamics spanning five years in freshwater bog lakes – Alexandra M Linz – bioRxiv

Occurrence of high-diversity metazoan- to microbial-dominated bioconstructions in a shallow Kimmeridgian carbonate ramp (Jabaloyas, Spain) – G San Miguel – Facies

Expression patterns of elemental cycling genes in the Amazon River Plume – Brandon M Satinsky – ISME Journal

Built environment

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes – Jiajiong Xu – Applied Microbiology and Biotechnology

Probiotics/prebiotics

Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models – In Young Hwang – Nature Communications

Review: Unraveling the Differences between Gram-Positive and Gram-Negative Probiotics in Modulating Protective Immunity to Enteric Infections – Sukumar Kandasamy – Frontiers in Immunology

Bioinformatics

* RTK: efficient rarefaction analysis of large datasets – Paul Saary – Bioinformatics

A geographically-diverse collection of 418 human gut microbiome pathway genome databases – Aria S Hahn – Scientific Data

Metabolomics

Indolepropionic acid and novel lipid metabolites are associated with a lower risk of type 2 diabetes in the Finnish Diabetes Prevention Study – Vanessa D de Mello – Scientific Reports

More microbes

Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells – Laura Rago – Bioelectrochemistry

Microbes in the news

Waste-munching bacteria could make nuclear stores safer – Sam Wong – New Scientist

‘Young poo’ makes aged fish live longer – Ewen Callaway – Nature

Microbiology: Gut microbes augment neurodegeneration – Daniel Erny – Nature

* This Artist Turns Sweat and Bacteria Into Art – Annie Tittiger – Wired

Science, publishing, and career

* Why do scientists fabricate and falsify data? A matched-control analysis of papers containing problematic image duplications – Daniele Fanelli – bioRxiv

Amy’s non-microbiology picks

Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity – Danish Saleheen – Nature

April 12, 2017

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A pretty broad Digest today, with a promising phylogenetic marker for fungal community studies, a new issue of the Journal of Microbiological Methods, and several news pieces, including one about brain stimulating for weight loss.

Jobs

Microbiology Technician – Lonza America Inc

BMS Microbiology – South West England

General microbiology

*A new promising phylogenetic marker to study the diversity of fungal communities: the GLYCOSIDE HYDROLASE 63 gene – L. Pérez-Izquierdo – Molecular Ecology Resources

pH-Controlled Cerium Oxide Nanoparticle Inhibition of Both Gram-Positive and Gram-Negative Bacteria Growth – Ece Alpaslan – Scientific Reports

Human oral microbiome

The probiotics in dentistry: a narrative review – A.M. Pujia – European Review for Medical and Pharmacological Sciences

Human ear microbiome

Microbiomes of the normal middle ear and ears with chronic otitis media – Shujiro B. Minami – Laryngoscope

Human gut microbiome

PrePrint: Household triclosan and triclocarban exposure impacts the adult intestinal microbiome but not the infant intestinal microbiome – Jessica V. Ribado – bioRxiv

Corrigendum: Antibiotic treatment at delivery shapes the initial oral microbiome in neonates – Luisa F. Gomez-Arango – Scientific Reports

Seven versus 10 days antibiotic therapy for culture-proven neonatal sepsis: A randomised controlled trial – Smriti Rohatgi – Journal of Paediatrics and Child Health

Animal experiments

Metabolic adaptation to the aqueous leaf extract of Moringa oleifera Lam.-supplemented diet is related to the modulation of gut microbiota in mice – Xiaoyu Gao – Applied Microbiology and Biotechnology

Bioactive Molecule from Streptomyces sp Mitigates MDR Klebsiella pneumoniae in Zebrafish Infection Model – Lalitha Cheepurupalli – Frontiers in Microbiology

Animal microbiome

Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing – Mao Li – Scientific Reports

Plant, root and soil microbiome

Biological Control of Bacterial Fruit Blotch of Watermelon Pathogen (Acidovorax citrulli) with Rhizosphere Associated Bacteria – Mahesh Adhikari – The Plant Pathology Journal

Book Chapter: Ecological Restoration Techniques for Management of Degraded, Mined-Out Areas and the Role Played by Rhizospheric Microbial Communities – Prashant Pant & Pratibha Pant – Green Technologies and Environmental Sustainability

Abstract: Consistently inconsistent drivers of patterns of microbial diversity and abundance at macroecological scales – Hendershot JN – Ecology

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere – Sadaf Kalam – Journal of Basic Microbiology

Water and extremophile microbiome

Abstract: Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon – P. Behera – Science of the Total Environment

PDF: The Effects of Soil Environmental Factors on the Colonization of Marine Biocontrol Bacteria – Zenghai Bao – Journal of Residuals Science & Technology

Book chapter: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad & Juan M. Gonzalez – Microbial Applications Vol.1

Effects of short-term warming and altered precipitation on soil microbial communities in alpine grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance – Weixiong Lin – Ecotoxicology and Environmental Safety

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities – Heikki Mykrä – Oikos

Microbes in space

Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions – Giorgio Casaburi – Scientific Reports

Phages and viruses

iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus – Songbai Yang – Scientific Reports

Technology

Release of a new issue of the Journal of Microbiological Methods, with various technical articles of potential interest.

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models – Chao Ye – Scientific Reports

Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding – Panu Somervuo – Methods in Ecology and Evolution

Microbes in the news

DIRTY PINTS One in three pints served in pubs use ‘bad’ bacteria-filled beer because landlords aren’t cleaning the pumps properly – Sara Kamouni – The Sun

Melioidosis: More cases of potentially fatal bacterium from NT dirt emerge – Eleni Rousos – ABC News

*Magnetic brain stimulation causes weight loss – Tim Sandle – Digital Journal

5 Ways to Ruin Wine Before It’s Even Bottled – Laura Burgess – Vine Pair

A public health failure – Otago Daily Times

Study to develop faster detection of antibiotic resistance – Scoop

Microbes on the market

Superbugs receive a dual drug attack – Kate Dearling – The Badger Online

Breast Milk Helps In The Growth Of Microbes Beneficial To Human Colon, Best For Babies Too – Jezreel Smith – The Science Times

April 11, 2017

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In today’s Microbiome Digest the first interesting study comes not from bacteria but from virus domain. Examining the genomes within a sample from a wastewater treatment plant in Austria, Schulz et al. assembled a previously undiscovered giant virus genome with more genes encoding components of the protein translation machinery than in other giant viruses. The second highlighted  study introduces new oleaginous microalga as a new potential source of compounds for biotechnological applications.

Events and jobs

QC Microbiology Analyst – Dublin, Ireland

Assistant Lecturer in Microbiology – Sligo, Ireland

General microbiome

The genetics of human longevity: an intricacy of genes, environment, culture and microbiome – Serena Dato – Mechanisms of Ageing and Development

Pregnancy and early life

Correlation between early-life regulation of the immune system by microbiota and allergy development – Thomas Gensollen – Journal of Allergy and Clinical Immunology

Microbial Community Assembly And Metabolite Profile Of The Gut Microbiome In Extremely Low Birthweight Infants – Stephen Wandro – bioRxiv

Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum – Chihaya Yamada – Cell Chemical Biology

A Comparative Study of Oral Microbiota in Infants with Complete Cleft Lip and Palate or Cleft Soft Palate – Agnieszka Machorowska-Pieniążek – BioMed Research International

Effect of probiotics on digestibility and immunity in infants: A study protocol for a randomized controlled trial – Lingli Xiao – Medicine

Human respiratory microbiome

Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment? – Kian Fan Chung – Journal of Allergy and Clinical Immunology

Oral microbiome

Measuring nitrate reductase activity from human and rodent tongues – Khandaker Ahtesham Ahmed – Nitric Oxide

Streptococcal adhesin SspA/B analogue peptide inhibits adherence and impacts biofilm formation of Streptococcus mutans – Tatsuro Ito – PLOSOne

Characterization of growth inhibition of oral bacteria by sophorolipid using a microplate-format assay – Daniel K.Y. Solaiman – Journal of Microbiological Methods

Salivary microbiome of an urban Indian cohort and patterns linked to subclinical inflammation  – Aneesha Acharya – Oral Diseases

Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment – M.M. Nascimento – Journal of Dental Research

Human skin microbiome

Bacterial communities on facial skin of teenage and elderly Thai females – Naraporn Somboonna – Archives of Microbiology

Skin microbiome and mast cells – Satomi Igawa – Translational Research

Human vaginal microbiome
Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods

‘Anaerococcus mediterraneensis’ sp. nov., a new species isolated from human female genital tract – K. Diop – New Microbes and New Infections

Human gut microbiome

Functional relevance of microbiome signatures: The correlation era requires tools for consolidation – Ludovica F. Buttó – Journal of Allergy and Clinical Immunology

Physiochemical Tuning of Potent Escherichia coli Anti-Adhesives by Microencapsulation and Methylene Homologation – Dimitri Alvarez Dorta – ChemMedChem

Gut microbiota functions: metabolism of nutrients and other food components –  Ian Rowland – European Journal of Nutrition

Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS–based metabolomics approach – Eikan Mishima – Kidney International

Animal experiments

Starch-enriched diet modulates the glucidic profile in the rat colonic mucosa – Maria Gabriella Gabrielli – European Journal of Nutrition

The influence of diet on the grass carp intestinal microbiota and bile acids – Jing Zhang – Aquaculture Research

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves – D.E. Gomez – Journal of Veterinary Internal Medicine

Gut Microbiota Modulation Attenuated the Hypolipidemic Effect of Simvastatin in High-Fat/Cholesterol-Diet Fed Mice – Xuyun He – Journal of Proteome Research

 

Animal microbiome

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut – Clayton M. Small – Genome Biology and Evolution

The structured diversity of specialized gut symbionts of the New World army ants – Piotr Łukasik – Molecular Ecology

Microbial composition of spiny ants (Hymenoptera: Formicidae: Polyrhachis) across their geographic range – Manuela Oliveira Ramalho – BMC Evolutionary Biology

Plant, root, and soil microbiome

Isolation, identification, and environmental adaptability of heavy-metal-resistant bacteria from ramie rhizosphere soil around mine refinery – Jie Jiang – Biotech

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities – Stephanie D. Jurburg – Scientific Reports

Microbial community response to hydration-desiccation cycles in desert soil – Adam Šťovíček – Scientific Reports

Water and extremophile microbiome

Development of an economical, autonomous pHstat system for culturing phytoplankton under steady state or dynamic conditions – Rachel L. Golda – Journal of Microbiological Methods

Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods – Sarita Pudasaini – Frontiers in Microbiology

Subduction zone forearc serpentinites as incubators for deep microbial life – Oliver Plümper – PNAS

Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago) – G. Bortoluzzi – Geobiology

Microbial biotechnology

Characterization of a Chlorophyta microalga isolated from a microbial mat in Salar de Atacama (northern Chile) as a potential source of compounds for biotechnological applications – Gladys Hayashida – Phycological Research

Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae – Vineeta Rai – Scientific Reports

Food microbiology

Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland – Agnieszka Kalwasińska – Antonie van Leeuwenhoek

Probiotics / prebiotics

Genome Sequences of Potential Probiotic Lactobacillus rhamnosus Isolates from Human Infants – Jason W. Arnold – Genome Announcements

Phages and viruses

Review: Phage injection establishes CRISPR immunity – Shimona Starling – Nature Reviews Microbiology

Giant viruses with an expanded complement of translation system components – Frederik Schulz – Science

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

Techniques

Identification of microorganisms grown on chromogenic media by MALDI-TOF MS – Petra Lüthje – Journal of Microbiological Methods

The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli – Sylvia Omulo – Journal of Microbiological Methods

Chapter in the book: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad – Microbial Applications Vol.1

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling – Stefan A. Boers – Scientific Reports
Microbes in the news 

Bacteria to the Future – Mizzou News (University of Missouri)

April 9, 2017

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Today’s digest features interesting research on how keystone microbial taxa regulate invasion of pathogens in agricultural systems. Also, interesting pre-print on how the gut microbiome influences the lifespan of fish.

Human gut microbiome

De novo assembly of microbial genomes from human gut metagenomes using barcoded short read sequences. Moss. E. Biorxiv

Review: Updating on Gut Microbiota and its Relationship with the Occurrence of Necrotizing Enterocolitis (Review). Hosny, M. Human Microbiome Journal

Supplementation of Diet with Galacto-oligosaccharides Increases Bifidobacteria, but not Insulin Sensitivity, in Obese Prediabetic Individuals. Canfora, E. Gastroenterology

Independence of Gut Bacterial Content and Neonatal Necrotizing Enterocolitis Severity Barron, LK. Journal of Pediatric Surgery

Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS–based metabolomics approach. Mishima, E.Kidney International

Human skin microbiome

Semi-automated quantitative analysis of the human skin microbiome diversity  Kumagai, C. Journal of Dermatological Science

Human Skin Is the Largest Epithelial Surface for Interaction with Microbes. Gallo, R. Journal of Investigative Dermatology

Human milk microbiome

Human milk microbiome in urban and rural populations of India Yati, H. Meta Gene

Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum.Yamada, C. Cell Chemical Biology

Food  microbiome

Microbial metabolites derived from colonic fermentation of non-digestible compounds. Tabernero, M. Current Opinion in Food Science

High relative humidity pre-harvest reduces post-harvest proliferation of Salmonella in tomatoes . Devleesschauwer, B. Food Microbiology

Plant and soil microbiome

Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems. Trivedi, P. Soil Biology and Biochemistry 

In-depth analysis of core methanogenic communities from high elevation permafrost-affected wetlands. Yang, S. Soil Biology and Biochemistry

Strigolactones in Plant Interactions with Beneficial and Detrimental Organisms: The Yin and Yang. López-Ráez, JA. Trends in Plant Science

Animal microbiome

Regulation of Life Span by the Gut Microbiota in The Short-Lived African Turquoise Killifish. Smith, P. Biorxiv

Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast. AlZahal, O. Journal of Dairy Science

Organochloride pesticides modulated gut microbiota and influenced bile acid metabolism in mice. Liu, Q. Environmental Pollution

Growth performance of the very small rotifer Proales similis is more dependent on proliferating bacterial community than the bigger rotifer Brachionus rotundiformis. Le, DVB.  Aquaculture

Evidence of Campylobacter jejuni reduction in broilers with early synbiotic administration Baffoni, L. International Journal of Food Microbiology

Raspberry pomace alters cecal microbial activity and reduces secondary bile acids in rats fed a high-fat diet. Fotschki, B.The Journal of Nutritional Biochemistry

Rumen microbial and fermentation characteristics are affected differently by acarbose addition during two nutritional types of simulated severe subacute ruminal acidosis in vitro. Wang, Y. Anaerobe.

Metabolomics 

Targeting aggression in severe mental illness: The predictive role of genetic, epigenetic, and metabolomic markers   Manchia, M. Progress in Neuro-Psychopharmacology and Biological Psychiatry

Prebiotics/Probiotics 

A three-stage continuous culture approach to study the impact of probiotics, prebiotics and fat intake on faecal microbiota relevant to an over 60 s population. Liu. Y.Journal of Functional Foods

 

April 8, 2017

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General microbiome

Modeling The Consequences Of Heterogeneity In Microbial Population Dynamics – Helena Herrmann – BioRxiv

Human respiratory microbiome

16S rRNA Gene Sequencing Reveals Site-Specific Signatures Of The Upper And Lower Airways Of Cystic Fibrosis Patients – Sarah K. Lucas – BioRxiv

Review: Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment? – Kian Fan Chung – The Journal of Allergy and Clinical Immunology

Human skin microbiome

Toxification of polycyclic aromatic hydrocarbons by commensal bacteria from human skin – Juliane Sowada – Archives of Toxicology

Human gut microbiome

Long-term use of antibiotics and risk of colorectal adenoma – Yin Cao – Gut

Changes in Composition of the Gut Bacterial Microbiome after Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in a Pediatric Heart Transplant Patient – Kyle L. Flannigan – Frontiers in Cardiovascular Medicine

Animal experiments

Iron Supplements Modulate Colon Microbiota Composition and Potentiate the Protective Effects of Probiotics in Dextran Sodium Sulfate-induced Colitis – Marco Constante – Inflammatory Bowel Diseases

Animal microbiome

Intestinal microbiota of healthy and unhealthy Atlantic salmon Salmo salar L. in a recirculating aquaculture system – Chun Wang – Chinese Journal of Oceanology and Limnology

Identification and modes of action of endogenous bacteria in taphonomy of embryos and larvae – Justin L. Eagan – Palaios

Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity – Yan Zeng – AMB Express

Skin microbiota differs drastically between co-occurring frogs and newts – Molly C. Bletz – The Royal Society Open Science

Amphibian skin microbiota exhibits temporal variation in community structure but stability of predicted Bd-inhibitory function – Molly C Bletz – ISME

Plant, root, and soil microbiome

Characterization of a metagenome-derived protease from contaminated agricultural soil microorganisms and its random mutagenesis – Chengjian Jiang – Folia Microbiologica

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests – Luis E Castañeda – PeerJ

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates – Suchismita Ghosh – BMC Microbiology

Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria – Nagissa Mahmoudi – Environmental Microbiology

Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China – Bo Xu – Biogeosciences

Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration – Deepak Kumaresan – Scientific Reports

Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems – P. Trivedi – Soil Biology and Biochemistry

Water and extremophile microbiome

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater – William B. Ludington – PLOS ONE

Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i – Heather Fullerton – ISME

Performance and microbial community analysis in a modified anaerobic inclining-baffled reactor treating recycled paper mill effluent – Haider M. Zwain – Environmental Science and Pollution Research

Microbial formation of labile organic carbon in Antarctic glacial environments – H. J. Smith – Nature Geoscience

Review: Cryospheric science: The power of glacial microbes – Elizabeth B. Kujawinski – Nature Geoscience

Taxonomic composition of Lake Baikal bacterioneuston communities – A. D. Galach’yants – Microbiology

Performance and microbial population dynamics during stable operation and reactivation after extended idle conditions in an aerobic granular sequencing batch reactor – Qiulai He – Bioresource Technology

Comparative metagenomics reveals insights into the deep-sea adaptation mechanism of the microorganisms in Iheya hydrothermal fields – Hai-liang Wang – Journal of Marine Systems

Built environment

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City – Julia M. Maritz – PLOS ONE

Food microbiology

The Dynamic Microbiota Profile During Pepper (Piper nigrum L.) Peeling by Solid-State Fermentation – Qisong Hu – Current Microbiology

Molecular investigation of bacterial communities during the manufacturing and ripening of semi-hard Iranian Liqvan cheese – M. Ramezani – Food Microbiology

Identification of microbial communities, with a focus on foodborne pathogens, during kimchi manufacturing process using culture-independent and -dependent analyses – Hae-Won Lee – LWT – Food Science and Technology

Probiotics / prebiotics

Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial – Judit Villar-García – PLOS ONE

Phages and viruses

Taxonomic variability and functional stability in microbial communities infected by phages – Stilianos Louca – Environmental Microbiology

Bioinformatics

EzMap: A Simple Pipeline for Reproducible Analysis of the Human Virome – Patrick Czeczko – Bioinformatics

Microbes in the news

You Should Appreciate Germs – Bill Gates

Microbes on the market

The expanding ecosystem of microbiome startups – Juliet Preston – MedCity News

April 6, 2017

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Jobs

Microbial genomics expert : Basel, Switzerland via Nature Jobs

University Lecturer/University Senior Lecturer in Microbiology : Cambridge, United Kingdom via Nature Jobs

 

Microbiome Research

Review: Gut Microbiota Modulation and Its Relationship with Obesity Using Prebiotic Fibers and Probiotics: A Review  – Dinesh K. Dahiya – Frontiers in Microbiology

Mini-Review: Linking Diet to Colorectal Cancer: The Emerging Role of MicroRNA in the Communication between Plant and Animal Kingdoms – Manuela Del Cornò –  Frontiers in Microbiology

Comparative Analysis of the Gut Microbial Communities in Forest and Alpine Musk Deer Using High-Throughput Sequencing – Xiaolong Hu – Frontiers in Microbiology

Complex pectin metabolism by gut bacteria reveals novel catalytic functions – Didier Ndeh – Nature

State of the Art: The association of the skin microbiota with health, immunity and disease – Markus Egert – Clinical Pharmacology and Therapeutics

Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants – Chloe A Autran – Gut (BMJ)

Targeting the gut microbiota with inulin-type fructans: preclinical demonstration of a novel approach in the management of endothelial dysfunction  – Emilie Catry – Gut (BMJ)

Exposure to household furry pets influences the gut microbiota of infant at 3–4 months following various birth scenarios – Hein M. Tun – Microbiome (BMC)

 

Probiotics – Prebiotics

Antimicrobial Compounds Produced by Vaginal Lactobacillus crispatus Are Able to Strongly Inhibit Candida albicans Growth, Hyphal Formation and Regulate Virulence-related Gene Expressions – Shuai Wang – Frontiers in Microbiology

Oral administration of Lactobacillus gasseri SBT2055 is effective in preventing Porphyromonas gingivalis-accelerated periodontal disease – R. Kobayashi  – Scientific Reports

Commentary: Inulin prebiotic: is it all about bifidobacteria? – Sandrine Paule Claus – Gut (BMJ)

 

Extremophiles

Relative importance of chemoautotrophy for primary production in a light exposed marine shallow hydrothermal system – Gonzalo V. Gomez-Saez – Frontiers in Microbiology

The ecology of acidophilic microorganisms in the corroding concrete sewer environment – Xuan Li  – Frontiers in Microbiology

 

Pathogen Research

A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121 – Ken-Ichi Lee – Frontiers in Microbiology

Comprehensive Diagnosis of Bacterial Infection Associated with Acute Cholecystitis using Metagenomic Approach – Manabu Kujiraoka – Frontiers in Microbiology

In vitro transfer of methicillin resistance determinants mecA from methicillin resistant Staphylococcus aureus (MRSA) to methicillin susceptible Staphylococcus aureus (MSSA) – Asinamai Athliamai Bitrus – BMC Microbiology

Effects of Pseudomonas aeruginosa and Streptococcus mitis mixed infection on TLR4-mediated immune response in acute pneumonia mouse model – Chao Song – BMC Microbiology

Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus – Eva Novakova – Frontiers in Microbiology

Supplemental invasion of Salmonella from the perspective of Salmonella enterica serovars Kentucky and Typhimurium – Kevin Howe – BMC Microbiology

Whole-genome comparative analysis of Salmonella enterica serovar Newport strains reveals lineage-specific divergence – Jie Zheng  – Genome Biology and Evolution

 

Evolution

Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) – David W. Waite – Frontiers in Microbiology

Evolutionary dynamics of CRISPR gene drives – Charleston Noble – Science Advances

 

Methods

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling – Stefan A. Boers – Scientific Reports

A Novel Ultra High-Throughput 16S rRNA Amplicon Sequencing Library Preparation Method On The Illumina HiSeq Platform – Eric J. de Muinck – BioRxiv

Improving ancient DNA genome assembly – Alexander Seitz  – PeerJ (peer-reviewed)

 

Bioinformatic Tools

ATLAS (Automatic Tool for Local Assembly Structures) – a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data – Richard Allen White III – PeerJ Preprints

 

News

Science Article Post: Ph.D. students face significant mental health challenges –  Elisabeth Pain

News: A deep dive into the genomes of penicillin fungi reveals a trove of potential drugs via Cosmos Magazine

 

April 5, 2017

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Today’s digest features interesting research on the dynamic microbiome evolution in social bees and the alteration in quorum Sensing, cell motility, stress Response, and carbohydrate metabolism  of gut microbiome by the organophosphate pesticide Diazinon. Low dose penicillin in early life can induce long term changes in mice gut microbiota, brain cytokines and behavior. Interesting reviews on the microbiome and human biology, and role of gut microbiota in the development of hypertension, including that associated with obstructive sleep apnea.

General microbiome

*Review: The Microbiome and Human Biology – Rob Knight – Annual Review of Genomics and Human Genetics

*Dynamic microbiome evolution in social bees – Waldan K. Kwong – Science Advances

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV – Leopoldo N. Segal – Cell Host & Microbe

Pregnancy and early life

Vancomycin treatment is a risk factor for vancomycin-nonsusceptible Staphylococcus capitis sepsis in preterm neonates – Marine Butin – Clinical Microbiology and Infection

Human oral microbiome

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis – Shinya Kageyama – Plos One

Review: Biofilm over teeth and restorations: What do we need to know? – Nancy J. Lin – Dental Materials

Human skin microbiome

Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes – Jennifer K. Plichta – Shock

Human gut microbiome

Review : The gut microbiota: a possible factor influencing systemic lupus erythematosus – Hadar Neuman – Current Opinion in Rheumatology

*Organophosphate Diazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome – Bei Gao -Toxicological Sciences

Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab – N. Chaput – Oncology

*Review: Obstructive Sleep Apnea-Induced Hypertension: Role of the Gut Microbiota – David J. Durgan – Current Hypertension Reports

Review: The Gut Microbiota and Alzheimer’s Disease – Chunmei Jiang – Journal of Alzheimer’s Disease

Fecal Microbiota Transplantation

Fecal Microbiota Transplantation in Patients with Blood Disorders Inhibits Gut Colonization with Antibiotic-Resistant Bacteria: Results of a Prospective, Single-Center Study – Jaroslaw Bilinski – Clinical Infectious Diseases

Animal microbiome

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes – Tongtong Li – Frontiers in Microbiology

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen – Henk J. van Lingen – Frontiers in Microbiology

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract – Dongyao Li – Scientific Reports

Animal experiments

Bifidobacterium in the gut microbiota confer resilience to chronic social defeat stress in mice – Chun Yang – Scientific Reports

Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni – Alexandre Thibodeau – Frontiers in Microbiology

Review : Outstanding animal studies in allergy II: from atopic barrier and microbiome to allergen-specific immunotherapy – Erika Jensen-Jarolim – Current Opinion in Allergy & Clinical Immunology

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice – Eveliina Munukka – ISME Journal

*Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior –  Sophie Leclercq – Nature Communications

Nod2 and Nod2-regulated microbiota protect BALB/c mice from diet-induced obesity and metabolic dysfunction – Ivan Rodriguez-Nunez – Scientific Reports

Plant, root, and soil microbiome

Aluminum-tolerant bacteria improve the plant growth and phosphorus content in ryegrass grown in a volcanic soil amended with cattle dung manure – María de la Luz Mora- Applied Soil Ecology

Invisible but consequential: root endophytic fungi have variable effects on belowground plant–insect interactions – Huyijuie Gan – Ecosphere

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China – Qin Tian – Scientific Reports

Phylogenetic conservation of substrate use specialization in leaf litter bacteria – Kristin L. Dolan – Plos ONE

Root biomass and exudates link plant diversity with soil bacterial and fungal biomass – Nico Eisenhauer – Scientific Reports

Water and extremophile microbiome

Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters – Laurie Favre – Journal of Proteome Research

Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria – Christina Ferousi – Current Opinion in Chemical Biology

*Potential sources of bacteria colonizing the cryoconite of an Alpine glacier – Andrea Franzetti – PLOS ONE

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments – Jean-François Briand – Microbial Ecology

Metabolomics

Review: Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis – Marianne Manchester – Advances in Virus Research

Effect of Major Royal Jelly Proteins on Spatial Memory in Aged Rats: Metabolomics Analysis in Urine – Di Chen -Journal of Agricultural and Food Chemistry

Food microbiology

Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads – Erica Pontonio – Scientific Reports

Probiotics / prebiotics

Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum – Quésia S. Damaceno – Probiotics and Antimicrobial Proteins

Bioinformatics

SLIMM: species level identification of microorganisms from metagenomes – Temesgen Hailemariam Dadi – PeerJ

Techniques

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area – Kazuma Nakano – Human Cell

High-pressure microscopy for tracking dynamic properties of molecular machines – Masayoshi Nishiyama – Biophysical Chemistry

Gut Microbiome Standardization in Control and Experimental Mice – Kathy D. McCoy – Current Protocols in Immunology

Diastereomer-specific Quantification of Bioactive Hexosylceramides from Bacteria and Mammals – Johanna von Gerichten – Journal of Lipid Research

Microbes in the news

Genetically engineered microbes make their own fertilizer, could feed the world’s poorest

The Next Plague (5) Bacteria: The Coming And Going And Coming Again Of Bacterial Plagues

Latest Helicobacter pylori breakthrough could lead to eradication of bacteria

Science, publishing, and career

Journal editor calls for ‘culture change’ around clinical trial data

Anitha’s non-microbiology picks

In the quest of Planet 9

April 4, 2017

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General microbiome

Diversity of fungus-growing termites (Macrotermes) and their fungal symbionts (Termitomyces) in the semiarid Tsavo Ecosystem, Kenya – R Vesala – Biotropica

Indole signalling and (micro)algal auxins decrease the virulence of Vibrio campbellii, a major pathogen of aquatic organisms – Q Yang – Environmental Microbiology

Large population study shows that adolescents with celiac disease have an increased risk of multiple autoimmune and nonautoimmune comorbidities –  A Assa – Acta Paediatrica

In vitro fermentation of oat β-glucan and hydrolysates by fecal microbiota and selected probiotic strains – JL Dong – Journal of the Science of Food and Agriculture

 

Human gut microbiome

Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China – G Yu – International Journal of Cancer

 

Animal microbiome

Host species shapes the co-occurrence patterns rather than diversity of stomach bacterial communities in pikas – H Li – Applied Microbiology and Biotechnology

 

Plant, root and soil microbiome

Phylloplane bacteria increase the negative impact of food limitation on insect fitness – GL Olson – Ecological Entomology

Bodyguards: Pathogen-Derived Decoys That Protect Virulence Factors – JK Paulus – Trends in Plant Science

Response of the rhizosphere prokaryotic community of barley (Hordeum vulgare L.) to elevated atmospheric CO2 concentration in open-top chambers – M Szoboszlay – Microbiology Open

Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L. – F Wemheuer – Genome Announcements

Phytoremediation of Petroleum-Contaminated Soil in Association with Soil Bacteria – P Pokethitiyook – Phytoremediation

Phytoremediation of Salt-Impacted Soils and Use of Plant Growth-Promoting Rhizobacteria (PGPR) to Enhance Phytoremediation – KE Gerhardt – Phytoremediation

Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil – J Leite – Brazilian Journal of Microbiology

Effect of elevated nitrate on biodegradation of pentabromodiphenyl ether (BDE-99) and change in microbial communities during groundwater recharge with tertiary-treated municipal wastewater – Y Yan – International Biodeterioration & Biodegradation

The tale of a neglected energy source: Elevated hydrogen exposure affects both microbial diversity and function in soil – M Khdhiri – Applied and Environmental Microbiology

 

Water and extremophile microbiome

Production and persistence of bacterial and labile organic matter at the hypoxic water–sediment interface of the St. Lawrence Estuary – M Hébert – Limnology and Oceanography

Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria – S Muthusamy – Environmental Microbiology

Spatiotemporal dynamics of bacterial community composition in large shallow eutrophic Lake Taihu: High overlap between free-living and particle-attached assemblages – X Tang – Limnology and Oceanography

 

Built environment

Coarse-graining bacteria colonies for modelling critical solute distributions in picolitre bioreactors for bacterial studies on single-cell level – C Westerwalbesloh – Microbial Biotechnology

 

Phages and Virus

Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections – KA Lythgoe – Trends in Microbiology

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction – E Harrison – Molecular Ecology

 

Techniques

*Review: Bioelectrochemical Systems for Measuring Microbial Cellular Functions – HMM Selim – Electroanalysis

Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation – KNM Daeffler – Molecular Systems Biology

Impact of Contaminating DNA in Whole Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis – M Thoendel – Journal of Clinical Microbiology

Genomics and Metagenomics in Microbial Ecology: Recent Advances and Challenges  – T Narihiro – Microbes and Environments

A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam –  S Das – Genomics Data

Optimization of a bioassay to evaluate Escherichia coli stress responses – B Cunha – IEEE

 

More microbes

*Review: Shapeshifting to Survive: Shape Determination and Regulation in Caulobacter crescentus – SA Woldemeskel – Trends in Microbiology

 

Microbes in news

Antibiotic Resistant Bacteria Common in Diabetic Foot Ulcers – S Gupta – Endocrinology Advisor

Fighting Antibiotic-Resistant Bacteria in Food Animals – J Bartel – Veterinary Medicine News

Vets warn dog owners about potentially deadly bacteria lurking in water – A Lasker – Lifestyle

Magnetic brain stimulation causes weight loss by making gut bacteria healthier – The Endocrine Society – Science Daily

Vapour droplets from threatened orcas show pneumonia bacteria – Waterloo Region Record – TheRecord.com

Hitchhiking Earth bacteria could evolve to live on Mars – M Irving – New Atlas

Bionic leaf turns air, water, sunlight and bacteria into fertilizer – B Hays – UPI

Nicholls sophomore researches antibiotic-resistant bacteria – G Ohlmeyer – Houmatoday.com

What the Bacteria in Your Mouth May Reveal About Your Cancer Risk – SG Miller – Live Science

April 1, 2017

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Events and jobs

Asst/Assoc Collegiate-Track Clinical Microbiology Faculty – Virginia Tech

General microbiome

Salivary inflammatory markers and microbiome in normoglycemic lean and obese children compared to obese children with type 2 diabetes – Waleed F. Janem – PLOS ONE

Microbiome study finds children with type 2 diabetes more likely to have poor oral health – Ellen Goldbaum – Medical Xpress

Cross-talk among metabolic parameters, esophageal microbiota, and host gene expression following chronic exposure to an obesogenic diet – Nadeem O. Kaakoush – Scientific Reports

Review: Microbiome Tools for Forensic Science – Jessica L. Metcalf – Trends in Biotechnology

Book: Forensic Microbiology – David O. Carter

Review: The legacy of the past: effects of historical processes on microbial metacommunities – Máté Vass – Aquatic Microbial Ecology

Human respiratory microbiome

The microbiome and secondary lung disease in neuromuscular patients: Is it time to change our clinical practice? – Reply – Florian Stehling – Respirology

Human skin microbiome

Patterns in the skin microbiota differ in children and teenagers between rural and urban environments – Jenni Lehtimäki – Scientific Reports

Human vaginal microbiome

Transient microbiota exposures activate dormant Escherichia coli infection in the bladder and drive severe outcomes of recurrent disease – Nicole M. Gilbert – PLOS Pathogens

Vaginal bacteria can trigger recurrent UTIs, study shows – Science Daily

Human gut microbiome

Review: Diet and microbiota in inflammatory bowel disease: The gut in disharmony – Davy CM Rapozo – World Journal of Gastroenterology

The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level – Wiley Barton – Gut

Animal experiments

NLRP12 regulates gut microbiota to suppress intestinal inflammation – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Community structure of the gut microbiota in sympatric species of wild Drosophila – Vincent G. Martinson – Ecology Letters

Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq – Alexandra Grote – PLOS Neglected Tropical Diseases

Researchers profile symbiotic relationship between bacteria and filarial nematodes – Medical Xpress

The Bacterial Community Found on the surface Purple Martin (Progne subis) Eggs – Beth A. Potter – The Open Ornithology Journal

Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas – Ghaida Hadaidi – Scientific Reports

Plant, root, and soil microbiome

Relationship of microbial communities and suppressiveness of Trichoderma fortified composts for pepper seedlings infected by Phytophthora nicotianae – Margarita Ros – PLOS ONE

Two-year field monitoring shows little evidence that transgenic potato containing ABF3 significantly alters its rhizosphere microbial community structure – Ki Jung Nam – Journal of Ecology and Environment

Members of Gammaproteobacteria as indicator species of healthy banana plants on Fusarium wilt-infested fields in Central America – Martina Köberl – Scientific Reports

Review: From yogurt to yield: Potential applications of lactic acid bacteria in plant production – John R. Lamont – Soil Biology and Biochemistry

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses – Tianzhu Li – PLOS ONE

Water and extremophile microbiome

Impact of selectively enriched microbial communities on long-term fermentative hydrogen production – R.K. Goud – Bioresource Technology

Co-invasion hypothesis explains microbial community structure changes in upland streams affected by riparian invader – Paul J. McInerney – Freshwater Science

Silver nanoparticles uptake by salt marsh plants – Implications for phytoremediation processes and effects in microbial community dynamics – Joana P. Fernandes – Marine Pollution Bulletin

Food microbiology

Identification of Microbial Profile of Koji Using Single Molecule, Real-Time Sequencing Technology – Wenyan Hui – Journal of Food Science

Probiotics / prebiotics

Roles of Probiotic Lactobacilli Inclusion in Helping Piglets Establish Healthy Intestinal Inter-environment for Pathogen Defense – Jiajun Yang – Probiotics and Antimicrobial Proteins

Phages and viruses

Review: Intriguing interaction of bacteriophage-host association: An understanding in the era of omics – Krupa M. Parmar – Frontiers in Microbiology

Bioinformatics

Review: Are Next-Generation Sequencing Tools Ready for the Cloud? – Antonio Celesti – Trends in Biotechnology

Techniques

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP) – Scott Tighe – Journal of Biomolecular Technology

In vitro gene expression-coupled bacterial cell chip for screening species-specific antimicrobial enzymes – Seok-Joon Kwon – Journal of Biotechnology and Bioengineering

Review: International Standards for Genomes, Transcriptomes, and Metagenomes – Christopher E. Mason – Journal of Biomolecular Technology

A comparison of sampling methods for examining the laryngeal microbiome – Alissa S. Hanshew – PLOS ONE

Microbes in the news

Probiotics For Babies: Why Your Baby’s Gut Health Is So Important –  Joy D’Souza – The Huffington Post Canada

NIH Wants to Test New Bacteria Therapy for Eczema – Maggie Fox – NBC News

Microbes on the market

Regulator OKs bacteria’s spread – Martin Cash – Winnipeg Free Press

March 31, 2017

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Microbiome research

Potential role of fecal microbiota from patients with slow transit constipation in the regulation of gastrointestinal motility – Xiaolong Ge, Scientific Reports

Opinion: Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet? – Eamonn M. M. Quigley – Nature Reviews Gastroenterology & Hepatology

Relevance of secretor status genotype and microbiota composition in susceptibility to rotavirus and norovirus infections in humans  – Jesús Rodríguez-Díaz – Scientific Reports

Milk Fat Globule Membrane Supplementation in Formula Modulates the Neonatal Gut Microbiome and Normalizes Intestinal Development – Ganive Bhinder – Scientific Reports

Critical Review: Microbiota-Gut-Brain Axis: Modulator of Host Metabolism and Appetite – Marcel van de Wouw – The Journal of Nutrition

Comparison of stool versus rectal swab samples and storage conditions on bacterial community profiles – Christine M. Bassis – BMC Microbiology

Ethnic and diet-related differences in the healthy infant microbiome – Jennifer C. Stearns – Genome Medicine (BMC)

Intestinal Barrier Function and the Gut Microbiome Are Differentially Affected in Mice Fed a Western-Style Diet or Drinking Water Supplemented with Fructose – Valentina Volynets – The Journal of Nutrition

The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation – Luis Gustavo de Almeida – PLOS One

Probiotics / Synbiotics

A comparative characterization of different host-sourced Lactobacillus ruminis strains and their adhesive, inhibitory, and immunomodulating functions – Xia Yu – Frontiers in Microbiology

Rice bran and Probiotics Alter the Porcine Large Intestine and Serum Metabolomes for Protection Against Human Rotavirus Diarrhea  – Nora Jean Nealon – Frontiers in Microbiology

Development of a synbiotic beverage enriched with bifidobacteria strains and fortified with whey proteins – Federico Baruzzi – Frontiers in Microbiology

Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics – Francis Cheng-Hsuan Weng – Frontiers in Microbiology

The effects of probiotic and synbiotic supplementation on metabolic syndrome indices in adults at risk of type 2 diabetes: study protocol for a randomized controlled trial – Nazila Kassaian – Trials (BMC)

Good Bugs vs Bad Bugs: Evaluation of Inhibitory Effect of Selected Probiotics against Enterococcus faecalis – Aarti A Bohora – The Journal of Contemporary Dental Practice (PDF here)

Probiotic bacteria prevent Salmonella – induced suppression of lymphoproliferation in mice by an immunomodulatory mechanism – R. Doug Wagner – BMC Microbiology

Exogenous lactobacilli mitigate microbial changes associated with grain fermentation (corn, oats, and wheat) by equine fecal microflora ex vivo – Brittany E. Harlow – PLOS One

 

Pathogens

Methicillin resistant Staphylococcus aureus emerged long before the introduction of methicillin in to clinical practice – Catriona Harkins – BioRxiv

Azathioprine, Mercaptopurine, and 5-Aminosalicylic Acid Affect the Growth of IBD-Associated Campylobacter Species and Other Enteric Microbes – Fang Liu –  Frontiers in Microbiology

Untargeted metabolomics analysis reveals key pathways responsible for the synergistic killing of colistin and doripenem combination against Acinetobacter baumannii – Mohd Hafidz Mahamad Maifiah – Scientific Reports

 

Other Genomics / Metagenomics

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning – John Vollmers – Frontiers in Microbiology

Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation – Sebastián N. Mendoza – Frontiers in Microbiology

Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains – Jimmy Do – Microbial Pathogenesis (Elsevier)

 

Bioinformatics

STITCHER 2.0: primer design for overlapping PCR applications  – Damien M. O’Halloran – Scientific Reports

 

Evolution

Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi – Juan Li – Scientific Reports

Evolutionary dynamics on any population structure – Benjamin Allen – Nature

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria – Rochelle M. Soo – Science

A perspective article about the latter paper here: How Cyanobacteria went green by Robert E. Blankenship

Structural reconstruction of protein ancestry – Romain Rouet – PNAS