December 13, 2017

Many interesting articles today: Probiotics can inhibit human colonic smooth muscle contraction in vitro in a dose dependent manner, arsenic exposure early in life alters the gut microbiome and can increase E.coli resistance genes, oral administration of two probiotics in mice has specific effects on gene expression in the small intestine, a detailed investigation of the impacts of Tcongolense infection in the tsetse fly, and multiple articles on plant and rhizosphere microbiome volatiles.

Events and jobs

Visiting Professor (Part Time) Microbiology  – Chamberlain College of Nursing, Jacksonville, FL Campus

Seminar: The “Bedside to Bench and Back Again” Paradigm in Gut Microbiome Research – Gary D. Wu – University of Chicago

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General microbiome

Review: Hygiene Hypothesis in Asthma Development: Is Hygiene to Blame? – Erik van Tilburg Bernardes – Archives of Medical Research

Human respiratory microbiome

Composition and variation of respiratory microbiota in healthy military personnel – Jun Hang – PLOS One

Human oral microbiome

Periodontitis is associated with significant hepatic fibrosis in patients with non-alcoholic fatty liver disease – William Alazawi – PLOS One

Human gut microbiome

Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study – Robert Šket – PLOS One

*Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh – Xiaoxi Dong – PLOS One

Editorial overview: Gastrointestinal: New frontiers in therapeutics for GI diseases and disorders — from microRNAs to novel pharmaceutics, to low FODMAP diets and microbiome – Fievos L Christofi – Current Opinion in Pharmacology

*Inhibition effect of Bifidobacterium longum, Lactobacillus acidophilus, Streptococcus thermophilus and Enterococcus faecalis and their related products on human colonic smooth muscle in vitro – Jing Gong – PLOS One

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Animal experiments

*The distinct effects of orally administered Lactobacillus rhamnosus GG and Lactococcus lactis subsp. lactis C59 on gene expression in the murine small intestine – Chise Suzuki – PLOS One

Diversity of intestinal bacterial lactase gene in antibiotics-induced diarrhea mice treated with Chinese herbs compound Qi Wei Bai Zhu San – Lu He – 3 Biotech

The Impact of Long-Term Intake of Phenolic Compounds-Rich Grape Pomace on Rat Gut Microbiota – Stéphanie Chacar – Journal of Food Science

Preprint: High-dimensional microbiome interactions shape host fitness – Alison L Gould – bioRxiv

Animal microbiome

Comparison of the intestinal mucosal microbiota in dogs siagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment – K. Kalenyak – FEMS Microbiology Ecology

*Molecular characterization of tsetse’s proboscis and its response to Trypanosoma congolense infection – Erick O. Awuoche – PLOS Neglected Tropical Diseases

Preprint: Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat – oren kolodny – BioRxiv

Plant, root, and soil microbiome

Pontibacter brevis sp. nov., isolated from rhizosphere soil of Tamarix ramosissima – Ghenijan Osman – International Journal of Systemic and Evolutionary Microbiology

*Volatiles in the Rhizosphere: Bioprospecting for Sustainable Agriculture and Food Security – Shyamalina Haldar – In: Volatiles and Food Security. Springer

*Characterization of Bacterial Volatiles and Their Impact on Plant Health Under Abiotic Stress – Anukool Vaishnav – In: Volatiles and Food Security. Springer

Dissertation: Plant growth-promoting rhizobacteria (PGPR) mediate interactions between abiotic and biotic stresses in cool- and warm-season grasses – Richard Coy – Auburn University

Endophytic Microorganisms: Promising Candidate as Biofertilizer – Manish Kumar – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

*Bacterial Volatiles in Promotion of Plant Under Biotic Stress – Shekhar Jain – In: Volatiles and Food Security. Springer

*Microbial Volatiles in Defense – Monika – In: Volatiles and Food Security. Springer

*Microbial Volatiles and Plant Defense – Kalaivani K. Nadarajah – In: Volatiles and Food Security. Springer

Wonders of Microbes in Agriculture for Productivity and Sustainability – Rajababu V. Vyas – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

Water and extremophile microbiome

Review: Marine microbiology: Illuminating the importance of nitrite oxidation – Ursual Hofer – Nature Reviews Microbiology

Microbial Ecology

Robustness of a model microbial community emerges from population structure among single cells of a clonal population – Anne W. Thompson – Environmental Microbiology

Resource availability modulates biodiversity-invasion relationships by altering competitive interactions – Tianjie Yang – Environmental Microbiology

Resistome

Action mechanism of naphthofuranquinones against fluconazole-resistant Candida tropicalis strains evidenced by proteomic analysis: The role of increased endogenous ROS – João Batista de Andrade Neto – Microbial Pathogenesis

Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen – Wei Gao – Current Opinion in Microbiology

Surveillance of antibiotic resistance among common Clostridium difficile ribotypes in Hong Kong – Viola C. Y. Chow – Scientific Reports

Food microbiology

Preprint: Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation – Jacob Steenwyk – bioRxiv

More Microbes

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence – Atteyet F. Yassin – PLOS one

PsrA controls the synthesis of the Pseudomonas aeruginosa quinolone signal via repression of the FadE homolog, PA0506 – Greg Wells – PLOS one

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Phages and viruses

Dissertation: Uncovering the Biological Features of Unknown Viruses Using Shotgun Metagenomic Sequence Data – Daniel Joseph Nasko – University of Delaware

Bioinformatics

MPA Portable: a Stand-alone Software Package for Analyzing Metaproteome Samples on the Go – Thilo Muth – Analytical Chemistry

Dissertation: Revealing Microbial Responses to Environmental Dynamics: Developing Methods for Analysis and Visualization of Complex Sequence Datasets – Matthew Kellom – Arizona State University

Preprint: Rarefaction, alpha diversity, and statistics – Amy Willis – bioRxiv

Biotechnology

Review: Electron transport phenomena of electroactive bacteria in microbial fuel cells: a review of Proteus hauseri – I-Son Ng – Bioresources and Bioprocessing

Dissertation: From Biofuels to Natural Products: Microbial Metabolic Engineering for Chemical Production – Nicole E Nozzi -University of California, Davis

Waste and Pollution

Assessment of a novel anti-biofouling microorganism (Bacillus sp. T5) for control of membrane biofouling and its effect on bacterial community structure in membrane bioreactors – Bahar Yavuztürk Gül – Water Science and Technology

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Microbes in the news

New Data: 2 Million Puerto Ricans Risk Water Contamination – Mekela Panditharatne – NRDC

Bacteria development marks new era in cellular design – Phys.org

Feeding Overcrowded Bacteria Increases Antibiotic Susceptibility – Genetic Engineering and Biotechnology News

A Bacterial Role In High Blood Pressure – The Microbiome Speaks – Chuck Dinerstein – American Council on Science and Health

New Microbiome Analysis Tool Resolves Individual Species, Strains – Rachel Lutz – MD Magazine

How honey bee gut bacteria help to digest their pollen-rich diet – EurekaAlert

Microbes on the market

Bio-Rad Inks Supply and Distribution Agreement for Microbiome MDx – genomeweb

Dannon, as a part of DanoneWave Public Benefit Corporation, Announces $50K in Grants for Graduate Studies – Markets Insider

 

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December 7, 2017

Meta-analysis of a collection of gut microbiome studies, characterization of two dandelion viruses, evaluation of an inclusive Research Education Community for engaging undergraduates in scientific research.

General microbiome

Bacterial social interactions and the emergence of community-intrinsic properties – Jonas Stenløkke Madsen – Current Opinion in Microbiology

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human gut microbiome

Gut microbiota in early life and its influence on health and disease: A position paper by the Malaysian Working Group on Gastrointestinal Health – Yeong Yeh Lee – Journal of Paediatrics and Child Health

Animal experiments

Moving beyond microbiome-wide associations to causal microbe identification – Neeraj K Surana – Nature

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungus causes increased condensed tannins concentrations in shoots but decreased in roots of Lotus japonicus L – Zakaria M Solaiman – Rhizosphere

Shifts in soil microbial community, soil enzymes and crop yield under peanut/maize intercropping with reduced nitrogen levels – Jun Chen – Applied Soil Ecology

Multifarious plant growth promotion by an entomopathogenic fungus Lecanicillium psalliotae – C M Senthil Kumar – Microbiological Research

Water and extremophile microbiome

Pre-print: Optogenetics reprogramming of planktonic cells for biofilm formation – Aiguo Xia – bioRxiv

Phages and viruses

Pre-print: Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses – Humberto J Debat – bioRxiv

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells – Timo A Lehti – Nature Communications

Bioinformatics

Pre-print: Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals – Almut Heinken – bioRxiv

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses – Claire Duvallet – Nature Communications

Techniques

In vitro enteroid-derived three-dimensional tissue model of human small intestinal epithelium with innate immune responses – Ying Chen – PLOS ONE

More microbes

Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects – Fausto Almeida – Nature Communications

Microbes in the news

Lemur study highlights role of diet in shaping gut microbiome – Erin Mckenney – Phys.Org

What Bacteria Can Tell Us About Human Evolution – Tara C Smith – Quanta Magazine

Duke launches new microbiome center, reflecting popularity of microbiome studies – Sean Cho – Duke Chronicle

Study shows first extensive and stable microbiome remodeling via B. infantis in infants – Weber Shandwick – EurekAlert

Air-eating bacteria found in Antarctica – Cosmos

The Microbes Making Themselves at Home on the Space Station – Marina Koren – The Atlantic

Microbes on the market

Breakthrough Evidence on Vomaris Bioelectric Technology’s Impact on Wound Biofilm Infection – PR Newswire

Precision Driven Health and Orion Health release Microbiome report – Voxy

Worldwide microbiome drugs market is likely to grow substantially by 2022 – Digital Journal

Science, career, and publishing

How to Keep Students in Science – Howard Hughes Medical Institute

An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning – David I Hanauer – PNAS

Pre-print: Assessing the Landscape of U.S. Postdoctoral Salaries – Rodoniki Athanasiadou – bioRxiv

Editorial: Great mentoring is key for the next generation of scientists – Nature

Amy’s non-microbiology picks

Organocalcium-mediated nucleophilic alkylation of benzene – Andrew S S Wilson – Science

November 30, 2017

A wide variety of interesting articles: Antibiotics administrated during labour impact  infant gut microbiome development, altered gut microbiome is related to liver function in individuals with Hep B, specific pathogens can alter social signaling in drosophila, a comphrensive study of the impact of diet on the lemur gut microbiome, a survey of antibiotic resistence genes in the drinking water across multiple continents, the impact of the hospital microbiome on the gut microbiome of preterm infants, the first evidence of a gut archeae impact on the host immune system, and two popular news articles refuting yesterday’s report of possible alien bacteria on the international space station.

Events and jobs

Web Developer, Microbiome Core – Harvard T.H. Chan School of Public Health

Account Manager – Microbiology –  South East England

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General microbiome

  • Health Economics and Regulations 

Faecal microbiota transplantation: a regulatory hurdle? – Frederick Verbeke – BMC Gastroenterology

Cost-effectiveness analysis of fecal microbiota transplantation for inflammatory bowel disease – Ting Zhang – Oncotarget

Pregnancy and early life

*Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants – Jennifer C. Stearns – Scientific Reports

Human skin microbiome

Skin Immune Landscape: Inside and Outside the Organism – Florence Abdallah – Mediators of Inflammation

Human gut microbiome
*Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients – Jing Wang – Frontiers in Microbiology

Faecal bacterial microbiota in patients with cirrhosis and the effect of lactulose administration – Aditya Narayan Sarangi – BMC Gastroenterology

Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection – Dina Kao – JAMA

Capsules for Fecal Microbiota Transplantation in Recurrent Clostridium difficile Infection – Krishna Rao – JAMA

Review: Antibiotic therapy in neonates and impact on gut microbiota and antibiotic resistance development: a systematic review – Jon Widding Fjalstad – Journal of Antimicrobial Chemotherapy

Long-term proton pump inhibitor therapy leads to small bowel bacterial overgrowth as determined by breath hydrogen and methane excretion – Agnieszka Sieczkowska – Journal of Breath Research

Review: Impact of gut microbiota on drug metabolism: an update for safe and effective use of drugs – Keumhan Noh – Archives of Pharmacal Research

Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure – Sabina Horvat – Scientific Reports

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Animal experiments

Preprint: The Vibrio cholerae Type VI Secretion System Can Modulate Host Intestinal Mechanics to Displace Commensal Gut Bacteria – Savannah L Logan – bioRxiv

Genes and Gut Bacteria Involved in Luminal Butyrate Reduction Caused by Diet and Loperamide – Nakwon Hwang – Genes

Simultaneous delivery of antibiotics neomycin and ampicillin in drinking water inhibits fermentation of resistant starch in rats – Diana G. Carvajal-Aldaz – Molecular Nutrition and Food Research

Animal microbiome

*Pathogenic bacteria enhance dispersal through alteration of Drosophila social communication – Ian W. Keesey – Nature Communications

*Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs – E. A. McKenney – Gut Microbes

Impact of Dietary Galacto-Oligosaccharide (GOS) on Chicken’s Gut Microbiota, Mucosal Gene Expression, and Salmonella Colonization – Rebecca-Ayme Hughes – Frontiers in Veterinary Science

Dietary energy drives the dynamic response of bovine rumen viral communities – Christopher L. Anderson – Microbiome

Effect of microalgae on intestinal inflammation triggered by soybean meal and bacterial infection in zebrafish – Karina Bravo-Tello – PLOS ONE

In vivo effects of Allium cepa L. on the selected gut microflora and intestinal histomorphology in broiler – Sajidur Rahman – Acta Histochemica

Enteric Pathogens and Their Toxin-Induced Disruption of the Intestinal Barrier through Alteration of Tight Junctions in Chickens – Wageha A. Awad – Toxins

Plant, root, and soil microbiome

The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria – Olaf Tyc – Trends in Microbiology

Impact of peat mining, and restoration on methane turnover potentials and methane-cycling microorganisms in a northern bog – Max Reumer – Applied and Environmental Microbiology

Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex – Apichai Tuanyok – Applied and Environment Microbiology

Water and extremophile microbiome
Functional Characterization of Probiotic Potential of Novel Pigmented Bacterial Strains for Aquaculture Applications – Sekar Jinendiran – Probiotics and Antimicrobial Proteins

Resistome

Preprint: Increased usage of antiseptics is associated with reduced susceptibility in clinical isolates of S. aureus – Katherine Hardy – bioRxiv

*Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey – Liping Ma – Microbiome

Review: Assessing the Risk of Antibiotic Resistance Transmission from the Environment to Humans: Non-Direct Proportionality between Abundance and Risk – Célia M. Manaia – Trends in Microbiology

Built environment

*Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome – Brandon Brooks – Nature Communications

Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells – Daniel Lipus – Applied and Environment Microbiology

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Microbial Ecology

Effect of Antimicrobial and Physical Treatments on Growth of Multispecies Staphylococcal Biofilms – Elizabeth J. Stewart – Applied and Environment Microbiology

More Microbes

  • Archaea

*Associated Archaeon Methanosphaera stadtmanae Is Recognized through Its RNA and Induces – Tim Vierbuchen – Frontiers in Immunology

  • Synthetic Microbes

Analysis and Implementation of a Multicellular Feedback Control Strategy in a Synthetic Bacterial Consortium – Gianfranco Fiore – ACS Synthetic Biology

Techniques

Diazotroph community characterization via a high-throughput nifH amplicon sequencing and analysis pipeline – John Christian Gaby – Applied and Environmental Microbiology

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes – Elin Videvall – mSystems

Generation of bacteriophage-insensitive mutants of Streptococcus thermophilus using an antisense RNA CRISPR-Cas silencing approach – Brian McDonnell – Applied and Environmental Microbiology

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Microbes in the news

*Bacteria on Space Station Likely From Germy Humans, Not Aliens – Elaina Zachos – National Geographic

*We are basically positive that the Russians did not find alien bacteria in space – Mary Beth Griggs – Popular Science

Custom Bacteria Make New Molecules On Demand – Sam Lemonick – Forbes

Toilet art sheds light on gut health – Newshub

November 28, 2017

Identification of nitrite-oxidizing bacteria important for dark ocean carbon fixation, effects of antibiotic exposure to the maternal gut microbiota extend to offspring in mice and enhance colitis, a review on genome mining for natural products discovery.

Events and jobs

Postdoc position on biofilm-mediated co-evolution of industrial strains – Biologisk Institut, University of Copenhagen, Denmark

Human skin microbiome

Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study – Lindsay Kalan – PLOS ONE

Human gut microbiome

Pre-print: Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean M Kearney – bioRxiv

Opinion: Human Gut Microbiome: Function Matters – Anna Heintz-Buschart – Trends in Microbiology

Review: The gut microbiome, symptoms, and targeted interventions in children with cancer: a systematic review – Jinbing Bai – Supportive Care in Cancer

Animal experiments

Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice – Anjelique F Schulfer – Nature Microbiology

Canagliflozin reduces plasma uremic toxins and alters the intestinal microbiota composition in a chronic kidney disease mouse model – Eikan Mishima – American Journal of Physiology, Renal Physiology

Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens – Luca Borrelli – Scientific Reports

Animal microbiome

Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing – Yu Guan – AMB Express

Plant, root, and soil microbiome

Pre-print: The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – bioRxiv

Water and extremophile microbiome

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation – Maria G Pachiadaki – Science

Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation – Bingjian Cui – Journal of Environmental Sciences

Phages and viruses

Review: Viruses of archaea: Structural, functional, environmental and evolutionary genomics – Mart Krupovic – Virus Research

Bioinformatics

Review: Omics-based natural product discovery and the lexicon of genome mining – Henrique Machado – Current Opinion in Microbiology

More microbes

Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris – Glenna J Kramer – BMC Genomics

Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism – Cristian Botta – Scientific Reports

Microbes in the news

Researchers conduct novel wheat microbiome analysis under four management strategies – Phys.Org

Fertility clinics treat abnormal vaginal bacteria aiming to improve reproductive outcome – Medical Xpress

Microbe threat to Mars – Andrew Masterson – Cosmos

Flies’ Feet Can Spread Bacteria – Kerry Grens – The Scientist

Despite Their Tiny Genome, A Beetle’s Bacteria Pack A Big Punch – Julianna LeMieux – American Council on Science and Health

CRISPR Harnessed to Turn Bacteria into Microscopic Tape Recorders – Genetic Engineering & Biotechnology News

Bacteria hysteria

Warning: Those lipstick samples could be loaded with poop, investigation finds – Mandy Matney – Sacramento Bee

Science, career, and publishing

Pre-print: A design framework and exemplar metrics for FAIRness – Mark D Wilkinson – bioRxiv

November 21, 2017

A review discussing metabolic-flux dependent regulation in microbes, diversity of coral-associated viral communities, what an Antarctic fungus can tell us about astrobiology.

General microbiome

Pre-print: Extending species-area relationships (SAR) to diversity-area relationships (DAR)© – Zhanshan Ma – aRxiv

Beneficial microbiomes: Biodiversity and potential biotechnological applications for sustainable agriculture and human health – Ajar Nath Yadav – Journal of Applied Biology and Biotechnology

Pregnancy and early life

Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full-term infants – Anuradha Ravi – FEMS Microbiology Ecology

Human respiratory microbiome

Pre-print: Dynamics of the upper airway microbiome in the pathogenesis of asthma-associated persistent wheeze in preschool children – Shu Mei Teo – bioRxiv

Human gut microbiome

Pre-print: A perturbation model of the gut microbiome’s response to antibiotics – Liam P Shaw – bioRxiv

Animal experiments

Pre-print: Within host selection for faster replicating bacterial symbionts – Ewa Chrostek – bioRxiv

Plant, root, and soil microbiome

Molecular characterization of Associative N2 fixing bacterium isolated from the roots of Finger millet (Eleusine coracana L.) and its interaction effects with microbial consortia on growth and yield – G B Santosha Gowda – Research Journal of Biotechnology

Significance of temperature and water availability for soil phosphorus transformation and microbial community composition as affected by fertilizer sources – Dasheng Sun – Biology and Fertility of Soils

Water and extremophile microbiome

Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile – Maria Eugenia Farias – PLOS ONE

Phylogenetic diversity and distribution of bacterial and archaeal amoA genes in the East China Sea during spring – Takafumi Kataoka – Archives of Microbiology

Microbes in space

Resistance of an Antarctic cryptoendolithic black fungus to radiation gives new insights of astrobiological relevance – Laura Selbmann – Fungal Biology

Phages and viruses

Pre-print: Coral-associated viral communities show high levels of diversity and host auxiliary functions – Karen D Weynberg – PeerJ

Biological Control of Pectobacterium carotovorum Via Specific Lytic Bacteriophage – Eman Marei – Journal of Basic and Applied Scientific Research

Bioinformatics

Book chapter: Chapter 1 – Metagenomics: A Paradigm Shift in Microbiology – Andrey V Mardanov – Metagenomics

More microbes

Review: Metabolic-flux dependent regulation of microbial physiology – Athanosios Litsios – Current Opinion in Microbiology

Microbes in the news

High-salt diet throws microbiome out of whack – Katharine Sanderson – Chemical & Engineering News

Rare Bacterial Taxa May Play Outsize Role in Soil Microbiome Structure, Study Suggests – Genome Web

Forsyth Institute researcher Floyd Dewhirst named as AAAS Fellow – EurekAlert

What makes soil, soil? Researchers find hidden clues in DNA – Phys.Org

Microbes on the market

PathoQuest Announces Formation of Scientific Advisory Board – Business Wire

November 15, 2017

Virome analysis of bats and archaea, bioinformatics tools for metatranscriptomics analysis, using mass spectrometry for studying microbiome metabolomics.

General microbiome

Review: An integrative omics perspective for the analysis of chemical signals in ecological interactions – A E Brunetti – Chemical Society Reviews

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human respiratory microbiome

The role of the microbiome in childhood asthma – Giovanna Pisi – Immunotherapy

Human vaginal microbiome

Pre-print: A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth M Bik – bioRxiv

Human gut microbiome

Gut microbiota and body composition in anorexia nervosa inpatients in comparison to athletes, overweight, obese, and normal weight controls – Sabrina Mörkl – International Journal of Eating Disorders

Review: Gut Microbiota-Dependent Modulation of Energy Metabolism – C N Heiss – Journal of Innate Immunity

Animal experiments

Antimicrobial emulsifier – glycerol monolaurate induces metabolic syndrome, gut microbiota dysbiosis and systemic low-grade inflammation in low-fat diet fed mice – Zengliang Jiang – Molecular Nutrition and Food Research

A temperature sensitive Mycobacterium paragordonae induces enhanced protective immune responses against mycobacterial infections in the mouse model – Byoung-Jun Kim – Scientific Reports

Animal microbiome

Review: The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes – Angela E Douglas – Current Opinion in Insect Science

Plant, root, and soil microbiome

Brassica napus has a key role in the recovery of the health of soils contaminated with metals and diesel by rhizoremediation – Rafael G Lacalle – Science of the Total Environment

Water and extremophile microbiome

Purification of eutrophic water containing chlorpyrifos by aquatic plants and its effects on planktonic bacteria – Xing-Jian Xu – Chemosphere

Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor – M Landreau – FEMS Microbiology Letters

Pre-print: Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling – David M Needham – bioRxiv

Food microbiology

Pre-print: Fusicatenibacter Is Associated with Kefir Drinking – Richard Sprague – bioRxiv

Probiotics/prebiotics

A novel double-layer mucoadhesive tablet containing probiotic strain for vaginal administration: Design, development and technological evaluation – María Teresa Sánchez – European Journal of Pharmaceutical Sciences

Efficacy and Safety of a Multistrain Probiotic Formulation Depends from Manufacturing – Vito Trinchieri – Frontiers in Immunology

Phages and viruses

Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana – Arielle Salmier – PLOS ONE

Review: The enigmatic archaeal virosphere – David Prangishvili – Nature Reviews Microbiology

Bioinformatics

Old meets new: most probable number validation of metagenomic and metatranscriptomic datasets in soil – Tim H Mauchline – Letters in Applied Microbiology

Pre-print: AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome – Xiao-Tao Jiang – bioRxiv

Metabolomics

Review: Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders – Hemi Luan – Mass Spectrometry Reviews

Pre-print: Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function – Chase Clark – bioRxiv

Techniques

Evaluating in vitro culture medium of gut microbiome with orthogonal experimental design and metaproteomics approach – Leyuan Li – Journal of Proteome Research

More microbes

Pre-print: Chemotaxis allows bacteria to overcome host-generated reactive oxygen species that constrain gland colonization – Kieran D Collins – bioRxiv

Microbes in the news

Specimens of Earth’s Oldest Known Life Forms Have Been Discovered in Tasmania – Michelle Starr – Science Alert

Shape-shifting agent targets harmful bacteria in the stomach – Phys.Org

Opinion: Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? – Lito E Papanicolas – Trends in Microbiology

Microbes on the market

A Silicon Valley Startup Wants Women To Test Their Vaginal Microbiota At Home – Ellie Kincaid – Forbes

Seres teams with cancer heavyweights for microbiome-checkpoint inhibitor combination trial – Nick Paul Taylor – FierceBiotech

November 8, 2017

Photosynthesizing bacteria printed on paper, investigations of microbial communities in water dispensers and mines, a review on the health benefits of natural products from truffles.

Human respiratory microbiome

Review: Airway Microbiota and Allergic Diseases: Clinical Implications – Eman M Fouda – International Journal of Pulmonary and Respiratory Sciences

Human oral microbiome

Proton pump inhibitor alters oral microbiome in gastrointestinal tract of healthy volunteers – Tsuyoshi Mishiro – Journal of Gastroenterology and Hematology

Human gut microbiome

Gut Microbiota Interacts with Markers of Adipose Tissue Browning, Insulin Action and Plasma Acetate in Morbid Obesity – José María Moreno-Navarrete – Molecular Nutrition and Food Research

Is there a relationship between intestinal microbiota, dietary compounds, and obesity? – Joanna Kałużna-Czaplińska – Trends in Food Science and Technology

Animal experiments

Combination of quercetin and resveratrol reduces obesity in high-fat diet-fed rats by modulation of gut microbiota – Le Zhao – Food and Function

Post-weaning social isolation of rats leads to long-term disruption of the gut microbiota-immune-brain axis – Fionn Dunphy Doherty – Brain, Behavior, and Immunity

Host-microbiota interaction induces bi-phasic inflammation and glucose intolerance in mice – Antonio Molinaro – Molecular Metabolism

Obesogenic diet-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis – June-Chul Lee – PLOS ONE

Animal microbiome

Gut region influences the diversity and interactions of bacterial communities in pikas (Ochotona curzoniae and Ochotona daurica) – Huan Li – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Nitrate induction and physiological responses of two maize lines differing in nitrogen use efficiency: effects on N availability, microbial diversity and enzyme activity in the rhizosphere – Zeno Varanini – Plant and Soil

The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface – J R Halliwell – Scientific Reports

Co-existence of Rhizobia and Diverse Non-Rhizobial Bacteria in the Rhizosphere and Nodules of Dalbergia odorifera Seedlings Inoculated with Bradyrhizobium elkanii,Rhizobium multihospitium–like and Burkholderia pyrrocinia–like Strains – Junkun Lu – Frontiers in Microbiology

Diversity of endophytic bacteria from Piper spp. with antagonistic property against Phytophthora capsici causing foot rot disease in black pepper (Piper nigrum L.) – Nadiya Kollakkodan – Journal of Tropical Agriculture

Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests – Sten Anslan – Soil Biology and Biochemistry

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease – Hongwu Yang – Frontiers in Microbiology

Resource availability underlies the plant-fungal diversity relationship in a grassland ecosystem – Lauren C Cline – Ecology

Water and extremophile microbiome

Microflora Thermarum Atlas project: biodiversity in thermal spring waters and natural SPA pools – F Valeriani – Water Science and Technology: Water Supply

Modes of carbon xation in an arsenic and CO2-rich shallow hydrothermal ecosystem – Nolwenn Callac – Scientific Reports

Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea – Tiantian Yu – Applied Microbiology and Biotechnology

Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula – Catherine M Luria – Frontiers in Microbiology

Built environment

Role of microbial activity in Fe(III) hydroxysulfate mineral transformations in an acid mine drainage-impacted site from the Dabaoshan Mine – Yanping Bao – Science of the Total Environment

Investigation of microbial communities in water dispensers – Sangjung Park – Applied Biological Chemistry

Food microbiology

Review: Potential health benefits of natural products derived from truffles: A review – Seema Patel – Trends in Food Science and Technology

Probiotics/prebiotics

Review: The development of seaweed-derived bioactive compounds for use as prebiotics and nutraceuticals using enzyme technologies – Suvimol Charoensiddhi – Trends in Food Science and Technology

Phages and viruses

Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes – Judith Villager – The ISME Journal

Biodiversity of bacteriophages infecting Lactococcus lactis starter cultures – Joana Oliveira – Journal of Dairy Science

Bioinformatics

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks – Zhu Chengsheng – Nucleic Acids Research

Metabolomics

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database – Wailing Huang – Nucleic Acids Research

mVOC 2.0: a database of microbial volatiles – Marie C Lemfack – Nucleic Acids Research

Techniques

Comparison of DNA-fingerprinting (T-RFLP) and high-throughput sequencing (HTS) to assess the diversity and composition of microbial communities in groundwater ecosystems – Karsten Karczewski – Limnologica Ecology and Management of Inland Waters

More microbes

Review: Our microbes not only produce antibiotics, they also overproduce amino acids – Sergio Sanchez – The Journal of Antibiotics

Disruption of N-acyl-homoserine lactone-specific signalling and virulence in clinical pathogens by marine sponge bacteria – José A Gutiérrez-Barranquero – Microbial Biotechnology

Microbes in the news

Bacteria-Activated Wallpaper that Generates Electricity – Katharine Keane – Architect Magazine

US government approves ‘killer’ mosquitoes to fight disease – Emily Waltz – Nature News

Bacteria may help babies’ digestive tracts more than suspected, scientists find – EurekAlert

Using neutrons to study how resistant bacteria evolve – Phys Org

Researchers identify mechanisms through which H. pylori bacteria cause gastric cancer – News Medical Life Sciences

New model reveals possibility of pumping antibiotics into bacteria – EurekAlert

Microbes on the market

Seres Therapeutics Awarded Grant from CARB-X to Support Development of Microbiome Therapeutic Candidate – Business Wire

Michael J. Fox Foundation, 23andMe to Jointly Advance Parkinson’s Disease Research – Carolina Henriques – Parkinson’s News Today