Category Archives: Metabolomics

September 5, 2016

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A microbial ecosystem created by fracking.

Human gut microbiome

Note: “All 34 PD patients were on dopaminergic drugs” Short chain fatty acids and gut microbiota differ between patients with Parkinson’s disease and age-matched controls – Marcus M. Unger – Parkisonism & Related Diseases

Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients – Francesco Paroni Sterbini – Applied and Environmental Microbiology

Upcoming study: Influence of habitual dietary fibre intake on the responsiveness of the gut microbiota to a prebiotic: protocol for a randomised, double-blind, placebo-controlled, cross-over, single-centre study – Genelle Healey – BMJ Open

Plants, roots, and soil microbiome

Screen Shot 2016-09-05 at 2.12.43 PMMicrobial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales – Rebecca A. Daly – Nature Microbiology

Press: New genus of bacteria found living inside hydraulic fracturing wells – ‘Frackibacter’ one of dozens of microbes forming sustainable ecosystems there, study finds – EurekAlert

Air microbiology

Aerobiology of the built environment: Synergy between Legionella and fungi – Absar Alum – American Journal of Infection Control

Generic aspects of the airborne spread of human pathogens indoors and emerging air decontamination technologies – M. Khalid Ijaz – American Journal of Infection Control

Water treatment microbiology

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data – I. Stanimirova – Talanta

Point-of-use Unit Based on Gravity Ultrafiltration Removes Waterborne Gastrointestinal Pathogens from Untreated Water Sources in Rural Communities – Cristóbal Chaidez – Wilderness & Environmental Medicine

Bioinformatics

MMinte: an application for predicting metabolic interactions among the microbial species in a community – Helena Mendes-Soares – BMC Bioinformatics

Microbes in the news

Chickenpox Cases In The US Down Since 2-Dose Vaccine Program Began – Dianne Depra – Tech Times

Study shows that more people carry meningitis bacteria than previously thought – Meningitis Research Foundation

Respect the old but seek out the new: Direct 16S rRNA-seq from bacterial communities – Kelle Freel – The Molecular Ecology

Bacterial Leaf Streak, a new corn disease hitting Kansas – Vincent Marshall – Dodge City Daily Globe

Manuka proves best bacteria fighter – Rush and Mills, Whangaroa College students, investigated manuka (tea tree) oil, won a top prize at the recent Top Energy Far North Science and Technology Fair.– Stuff.co.nz

Fears CSIRO staff exposed to ‘low risk’ toxic bacteria at Canberra lab – ABC Australia

Microbes and you: a partnership millions of years old – Dyani LewisCosmos Magazine

September 3, 2016

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The gut microbiome of the American cockroach is as resilient as its host, two papers on polar microbes and climate changes, two JAMA papers about transcription-based tests to distinguish viral from bacterial infections in children, and sampling Jeremy Bentham’s preserved body.

Events

7th edition of the International Course in Microbial Ecology – Publishing Dos and Don’ts for Microbial Ecologists – October 2016, Catania, Italy

Human vaginal microbiome

Alterations of the vaginal microbiota in the third trimester of pregnancy and pPROM –
C. Genovese – Eur Rev Med Pharmacol Sci

Human gut microbiome

Review: The gut microbiota: A treasure for human health – Daotong Li – Biotechnology Advances

Editorial: The Human Gutome: Journey of Microbes and Health – Dimiter Dimitrov – Frontiers in Genetics

Animal microbiome

The core gut microbiome of the American cockroach, Periplaneta americana, is stable and resilient to dietary shifts – Kara A. Tinker – Applied and Environmental Microbiology

Microbiome changes through ontogeny of a tick pathogen vector – Christine P. Zolnik – Molecular Ecology

Plant, root, and soil microbiome

Long-lasting effects of land use history on soil fungal communities in second-growth tropical rain forests – Benedicte Bachelot – Ecological applications

Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers – Sarah M. Allarda – Science of the Total Environment

Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture – Yuan Qin – Biotechnology Advances

Extremophile microbiome

Polar Marine Microorganisms and Climate Change – C. Verde – Advances in Microbial Physiology

Antarctic microbial communities are functionally redundant, adapted and resistant to short term temperature perturbations – S.Z. de Scally – Soil Biology and Biochemistry

Metabolomics and other techniques

The future of NMR-based metabolomics – John L Markley – Current Opinion in Biotechnology

Microfluidics in microbiology: putting a magnifying glass on microbes – Sanya Siddiqui – Integrative Biology

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists– Praveen Rahi – Frontiers in Microbiology

More microbiology

Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children – Jethro A. Herberg – JAMA

Association of RNA Biosignatures With Bacterial Infections in Febrile Infants Aged 60 Days or Younger – Prashant Mahajan – JAMA

Microbes in the news

The Good Gut: Discussing the stomach’s world of disease-fighting microbes – Paul Costello – Stanford Medicine

San Francisco has a crazy plan to fight pee stink with bacteria-eating enzymes – Urine trouble – Rachel Becker – The Verge

MSU researchers noted for approach to studying bacteria and viruses that live in human gut – Evelyn Boswell – MSU News Service

Yum! Digesting ASM resources for food microbiology – Julie Wolf – American Society for Microbiology

Have you ever wondered what sorts of bacteria and fungi are lurking on Jeremy Bentham? Dr Adam Roberts, thanks to UCL Collections, visited Jeremy Bentham to see if he could find any interesting bacteria. – University College of London

I Contain Multitudes by Ed Yong review – we are possessed by bacteria – Tim Radford – The Guardian

Gaming for Gut Research – American Gut researchers developed Colony B, an app that is both a fun game and a way “citizen scientists” can contribute to microbiome data analysis – UC San Diego Health Sciences News

 

August 29, 2016

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Breast milk protects against GBS colonization, niche segregation in the gut, drug detection and effects in streams, reconstruction of metabolic networks.

Pregnancy and birth

Role of human milk oligosaccharides in Group B Streptococcus colonisation – Nicholas J Andreas – Clinical & Translational Immunology

Press: Breast Milk Sugar May Protect Newborns Against Deadly Bacterial Infection – Dianne Depra – Tech Times

Human skin microbiome

News and Views: Microbiome: Ecology of eczema – Ian D. Odell – Nature Microbiology

Human respiratory microbiome

Changes in the prevalence and biofilm formation of Haemophilus influenzae and Haemophilus parainfluenzae from the respiratory microbiota of patients with sarcoidosis – Urszula Kosikowska – BMC Infectious Diseases

Human vaginal microbiome

The cervico-vaginal microbiota in women notified for Chlamydia trachomatis infection: A case-control study at the STI outpatient clinic in Amsterdam, the Netherlands – C van der Veer – Clinical Infectious Diseases

Human gut microbiome

Transcriptional interactions suggest niche segregation among microorganisms in the human gut – Damian Rafal Plichta – Nature Microbiology

Review: Alzheimer’s disease and gut microbiota – Xu Hu – Science China Life Sciences

Review: In Sickness and in Health: The Relationships Between Bacteria and Bile in the Human Gut – A.J. Hay – Advances in Applied Microbiology

Animal experiments

Enterococcus faecalis readily colonizes the entire gastrointestinal tract and forms biofilms in a germ-free mouse model – Aaron M.T. Barnes – Virulence

Animal microbiome

Distinct Bacterial Microbiomes in Sexual and Asexual Potamopyrgus antipodarum, a New Zealand Freshwater Snail – Cristina Takacs-Vesbach – PLOS ONE

Water and extremophile microbiome

Occurrence and Potential Biological Effects of Amphetamine on Stream Communities – Sylvia S. Lee – Environmental Science & Technology

Press: Ecological consequences of amphetamine pollution in urban streams – Cary Institute
Your drain on drugs: Amphetamines seep into Baltimore’s streams – Jen Christensen – CNN
Comment from PubMed Commons by Daniel Himmelstein 

Diversity of culturable bacteria recovered from Pico Bolívar’s glacial and subglacial environments, at 4950 m, in Venezuelan tropical Andes – Johnma Rondón – Canadian Journal of Microbiology

Metabolomics

Efficient Reconstruction of Predictive Consensus Metabolic Network Models – Ruben G. A. van Heck – PLOS Computational Biology

Bioinformatics and Metagenomics

Review: Toward Accurate and Quantitative Comparative Metagenomics – Stephen Nayfach – Cell

Techniques

Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life – Soeren M Karst – bioRxiv

A method for assessing efficiency of bacterial cell disruption and DNA release – Olle M. de Bruin – BMC Microbiology

Microbes in the news

Findings from the American Physiological Society’s Inflammation, Immunity and Cardiovascular Disease conference: Targeting gut bacteria to reduce weight gain – Science Daily

Microbes at work in your Kimchi – Jennifer – The Microbial Menagerie

Artist’s 46-year-old loo paper to be studied: Billy Apple’s decades-old lavatory paper is now part of a scientific study at Auckland University – Jamie Morton – NZ Herald

BacteriaHysteria: The ultimate embodiment of modern day germophobia: Squix – Jonathan Eisen – MicroBEnet

Science misconduct

Leading scientist suspended amid misconduct claims: Robert Ryan, award-winning Scottish microbiologist now under investigation – Victoria Weldon – Herald Scotland

August 13, 2016

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Fracking, floating islands and a multivariate statistical framework.

Human respiratory microbiome

Editorial: Another piece in the ‘research mosaic’ that describes the role of the lung microbiome in COPD – Gary B Huffnagle – Thorax

Review: Toward revision of antimicrobial therapies in hematopoietic stem cell transplantation: target the pathogens, but protect the indigenous microbiota – Alexander Khoruts – Translational Research

Human urinary tract microbiome

Note: no mention of extraction controls. Does the Urinary Microbiome Play a Role in Urgency Urinary Incontinence and Its Severity? – Lisa Karstens – Frontiers in Cellular Infection Microbiology

Human gut microbiome

Review: Gut Microbiota: Modulation of Host Physiology in Obesity – Vandana Nehra – Physiology

Close encounters of the type‐six kind: injected bacterial toxins modulate gut microbial composition – Martina Sassone‐Corsi – EMBO Reports

Plant, root, and soil microbiome

Floating islands: Metagenomic approach to characterize soil microbial diversity of Phumdi at Loktak Lake – Sampada Puranik – Water Science & Technology

Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface – Paula J. Mouser – FEMS Microbiology Ecology

Isolation studies reveal a shift in the cultivable microbiome of oak affected with Acute Oak Decline – Sandra Denman – Systematic and Applied Microbiology

Arbuscular mycorrhizal fungal communities in forest plant roots are simultaneously shaped by host characteristics and canopy-mediated light availability – Kadri Koorem – Plant and Soil

Soil and plant components ecological stoichiometry in four steppe communities in the Loess Plateau of China – Quanchao Zeng – CATENA

Effect of cobalt and silver nanoparticles and ions on Lumbricus rubellus health and on microbial community of earthworm faeces and soil – Livia Vittori Antisari – Applied Soil Ecology

Bioreactor microbiology

Engineering artificial communities for enhanced FTOH degradation – Matthew Lewis – Science of the Total Environment

Metagenomics, phages and viruses, bioinformatics

Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria – Rohit Ghai – The ISME Journal

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities – Kim-Anh Lê Cao – PLOS ONE

Book: Algorithms in Bioinformatics. 16th International Workshop, WABI 2016, Aarhus, Denmark, August 22-24, 2016. Proceedings
Better Identification of Repeats in Metagenomic Scaffolding – Jay Ghurye –
Compact Universal k-mer Hitting Sets – Yaron Orenstein

Proteomics

Review: Environmental Microbial Community Proteomics: Status, Challenges and Perspectives – Da-Zhi Wang – Int J Mol Sci

Microbes in the news

Saving antibiotics for when they are really needed: the Dutch example – Tony Sheldon – BMJ

Could friendly bacteria be used to treat cancer? – Paul Dyson – The Conversation

August 12, 2016

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On vacation, so here is a short and late Digest for you: Metabolomics of preterm birth, mouse gut bacteria collection, bacteria associated with mosses.

Pregnancy and birth

Use of metabolomics for the identification and validation of clinical biomarkers for preterm birth: Preterm SAMBA – Jose G. Cecatti – BMC Pregnancy and Childbirth

Animal microbiome

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota – Ilias Lagkouvardos – Nature Microbiology

First public collection of bacteria from the intestine of mice. Mouse gut bacteria find a new home – Science Daily

Environment shapes the fecal microbiome of invasive carp species – Jessica J. Eichmiller – Microbiome

Plant, root, and soil microbiome

Comparative analysis of bacteria associated with different mosses by 16S rRNA and 16S rDNA sequencing – Yang Tian – Journal of Basic Microbiology

Water microbiome

A metabolomics guided exploration of marine natural product chemical space – Dimitrios J. Floros – Metabolomics

Bioreactor microbiome

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates – Irena Maus – Biotechnology for Biofuels

Food microbiology

Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation – Edward D. Kerr – PeerJ

Microbial Ecology and other

Compartmentalization in PVC super-phylum: evolution and impact – Sandrine Pinos – Biology Direct

Conflicts over host manipulation between different parasites and pathogens: Investigating the ecological and medical consequences – Nina Hafer – BioEssays

Microbes in the news

Soil Has a Microbiome, too. The unique mix of microbes in soil has a profound effect on which plants thrive and which ones die – Carrie Arnold – Smithsonian

Gut bacteria have own circadian clock – MedicalXpress

Not your momma’s microbe lab: a new genetic engineering machine takes microbial design to the masses – Casey Gilman – Philly.com

How brushing your teeth could prevent cancer: Twice daily scrub reduces bacteria linked to bowel tumours – Colin Fernandez – Daily Mail

Picture of the day: Metal-oxidizing bacteria from a gold mine – Science 360

Attendee Shares Experience from DDW® 2016 Active Learning Session on the Gut Microbiome – Gasto.org

Science, publishing, and career

The manterruption is real. Why Women Talk Less Than Men at Work – Alicia Adamczyk – Time / Money Magazine

Satire: First Draft of Peer-Review Rebuttal Just Says “Fuck Off” – The Allium

 

 

August 5, 2016

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Urinary tract microbiome, preterm gut microbiota and humanized mice, fungi of Crocus (Saffron plant), and bead-beating artefacts.

General microbiome

Introduction to special issue of Molecular Metabolism: Microbiota: ‘bugging’ insights into metabolic regulation – Thomas Schwarz-Romond – Molecular Metabolism

Human oral microbiome

Transcriptome Analysis of B Cell Immune Functions in Periodontitis: Mucosal Tissue Responses to the Oral Microbiome in Aging – Jeffrey L. Ebersole – Frontiers in Immunology

Human respiratory microbiome

Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung – Leopoldo N Segal – Thorax

Review: Microbiome in the pathogenesis of cystic fibrosis and lung transplant-related disease – Sushma K. Cribbs – Translational Research

Human urinary tract microbiome

Evaluation of the Urinary Microbiota of Women With Uncomplicated Stress Urinary Incontinence – Krystal J. Thomas-White – American Journal of Obstetrics and Gynecology

Human gut microbiome

Review: Microbiota as Mediator of Cancer Progression and Therapy – Jilian L. Pope – Translational Research

Review: The human microbiome in rheumatic autoimmune diseases: A comprehensive review – Patrick Coit – Clinical Immunology

Review: Human gut microbiota plays a role in the metabolism of drugs – Lenka Jourova – Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub

Animal experiments

Preterm infant gut microbiota affects intestinal epithelial development in a humanized gnotobiotic mouse model – Yueyue Yu – American Journal of Physiology – Gastrointestinal and Liver Physiology

Symbiotic gut commensal bacteria act as host cathepsin S activity regulators – Alex Steimle – Journal of Autoimmunity

Research Highlight (but very harsh title): Gut microbiota: Microbiota and behaviour: visiting the sins of the mother – Paul Forsythe – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research – Karina Gajardo – Scientific Reports

Plant, root, and soil microbiome

Molecular phylogeny, diversity, community structure and plant growth promoting properties of fungal endophytes associated with the corms of Saffron plant: an insight into the microbiome of Crocus sativus Linn – Zahoor Ahmed Wani – Fungal Biology

Leaf Treatments with a Protein-Based Resistance Inducer Partially Modify Phyllosphere Microbial Communities of Grapevine – Martina Cappelletti – Frontiers in Plant Science

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils – Xue Zhou – Frontiers in Microbiology

Fungus-associated bacteriome in charge of their host behavior – Kristin Schulz-Bohm – Fungal Genetics and Biology

Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control – Josefa Blaya – PLOS ONE

Water and extremophile microbiome

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris – Sonja Oberbeckmann – PLOS ONE

Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica – Heather N. Buelow – Frontiers in Microbiology

Microbial community structure shifts are associated with temperature, dispersants and nutrients in crude oil-contaminated seawaters – Long Meng – Marine Pollution Bulletin

Bioinformatics and metagenomics

Rapid resistome mapping using nanopore sequencing – Eric van der Helm – bioRxiv

Metabolomics

Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena – Jinchun Sun – Toxicology in Vitro

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future – S. Barnes – Journal of Mass Spectrometry

Techniques

Bead-beating artefacts in the Bacteroidetes to Firmicutes ratio of the human stool metagenome – Heidi C. Vebø – Journal of Microbiological Methods

Pipeline for amplifying and analyzing amplicons of the V1–V3 region of the 16S rRNA gene – Heather K. Allen – BMC Research Notes

A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics – Risa Takagi – PLOS ONE

More microbiology

Metabolic engineering of microbial competitive advantage for industrial fermentation processes – A. Joe Shaw – Science

Microbes in the news

AGA establishes NIH-funded registry to track fecal microbiota transplants – EurekAlert

Maternal microbial inheritance—benefits of breastfeeding – Md Zohorul Islam

ASM Agar Art Calendar 2016/2017

Science, publishing, and career

What Is the Key Best Practice for Collaborating with a Computational Biologist? – Cell Systems

University of Waterloo boosts salaries of female faculty after discrepancy found – Paola Loriggio – CP24

Bik’s Non-Microbiology Picks

Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits – Hagop S. Atamian – Science
How do sunflowers follow the Sun—and to what end? – Winslow R. Briggs – Science

August 1, 2016

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Storage conditions of infant fecal microbiota, microbial pinnacles, bioaerosols in chicken production facilities.

General microbiome

Special issue of Microbial Biotechnology, including:
Biome engineering-2020 – Harald Brüssow
Microbial bioinformatics 2020 – Mark J. Pallen
Next-generation studies of microbial biofilm communities – Scott A. Rice
Plant–microbe partnerships in 2020 – Birgit Mitter

Opinion: Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut – Eveline Adam – Frontiers in Microbiology

Pregnancy and birth

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room? – Alexander G Shaw – Microbiome

Gut Microbiota Richness and Composition and Dietary Intake of Overweight Pregnant Women Are Related to Serum Zonulin Concentration, a Marker for Intestinal Permeability – Kati Mokkala – The Journal of Nutrition

Review: Microbial Changes during Pregnancy, Birth, and Infancy – Meital Nuriel-Ohayon – Frontiers in Microbiology

Human eye microbiome

Ocular surface microbiome in meibomian gland dysfunction in Auckland, New Zealand –
Grant A. Watters – Clinical & Experimental Ophtalmology

Human gut microbiome

Microbial diversity in individuals and their household contacts following typical antibiotic courses – Shira R. Abeles – Microbiome

Microbial Factors Associated with Post-Operative Crohn’s Disease Recurrence – Emily K Wright – Journal of Crohn’s and Colitis

Efficacy of antineoplastic treatment is associated with the use of antibiotics that modulate intestinal microbiota – Natali Pflug – OncoImmunology

Review: The oesophageal microbiome: an unexplored link in obesity-associated oesophageal adenocarcinoma – Nadeem O. Kaakoush – FEMS Microbiology Ecology

Review: Normal, Regular and Standard: Scaling the Body through Fecal Microbial Transplants – Matthew J. Wolf-Meyer – Medical Anthropology Quarterly

Review: Gut Microbiota Imbalance and Base Excision Repair Dynamics in Colon Cancer – Debolina Ray – Journal of Cancer

Review: Fine-Tuning Cancer Immunotherapy: Optimizing the Gut Microbiome – Jonathan M. Pitt – Cancer Research

Review: Irritable bowel syndrome, the microbiota and the gut-brain axis – Hans Raskov – Gut Microbes

Animal microbiome

Fish: Alterations of the gut microbiome of largemouth bronze gudgeon (Coreius guichenoti) suffering from furunculosis – Tongtong Li – Scientific Reports

Plant, root, and soil microbiome

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation – Adria L. Fernandez – Applied Microbiology and Biotechnology

Correlation analysis of enzyme activities and deconstruction of ammonia-pretreated switchgrass by bacterial-fungal communities – Abhiney Jain – Bioresource Technology

Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach – Y.C. Li – Journal of Applied Microbiology

High culturability of epiphytic bacteria and frequency of biosurfactant producers on leaves – Adrien Y. Burch – Applied and Environmental Microbiology

Desiccation of sediments affects assimilate transport within aquatic plants and carbon transfer to microorganisms – Isabell von Rein – Plant Biology

Review: Emergence of plant and rhizospheric microbiota as stable interactomes – Prasun Bandyopadhyay – Protoplasma

Water and extremophile microbiome

Growth of elaborate microbial pinnacles in Lake Vanda, Antarctica – D. Y. Sumner – Geobiology

Diversity and succession of autotrophic microbial community in high-elevation soils along deglaciation chronosequence – Jinbo Liu – FEMS Microbial Ecology

Air microbiome

High throughput genomic sequencing of bioaerosols in broiler chicken production facilities – Kate M. O’Brien – Microbial Biotechnology

Bioinformatics

RevEcoR: an R package for the reverse ecology analysis of microbiomes – Yang Cao – BMC Bioinformatics

Metabolomics

Review: Metabolites: messengers between the microbiota and the immune system – Maayan Levy – Genes & Development

Techniques

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering – Geoffrey L. House – Applied and Environmental Microbiology

Microbes in the news
Why is microbiome so important? Gut instinct tells you – Jessica le Roux – FoodMed

Science, publishing, and career

Intentional equity – France A. Córdova – Science

Lost in Translation: From scientists to the press and to the public – The Microbial Menagerie

July 26, 2016

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The last common ancestor, pika gut microbiome, fire-fighting chemicals and soil microbiome, improved Illumina-compatible 18S rRNA primers.

Jobs

Verily (Google-associated) is looking for a Microbiome Research Associate

Pregnancy and birth

Probiotic properties of lactic acid bacteria isolated from human milk – N.A. Reis – Journal of Applied Microbiology

Human oral microbiome

High Throughput Quantitative Method for Assessing Coaggregation among Oral Bacterial Species – Elizabeth Levin-Sparenberg – Letters in Applied Microbiology

Periodontal infectogenomics: systematic review of associations between host genetic variants and subgingival microbial detection – Luigi Nibali – Journal of Clinical Periodontology

Human respiratory microbiome

Upper airway viruses and bacteria and clinical outcomes in children with cough – Kerry-Ann F. O’Grady – Pediatric Pulmonology

Human skin microbiome

Hypothesis: The skin microbiome: Is it affected by UV-induced immune suppression? – Vijaykumar Patra – Frontiers in Microbiology

Human gut microbiome

Gut microbiota-host interactions and juvenile idiopathic arthritis – Miika Arvonen – Pediatric Rheumatology

Designing fecal microbiota transplant trials that account for differences in donor stool efficacy – Scott W. Olesen – bioRxiv

Probiotics and the Microbiome in Celiac Disease: A Randomised Controlled Trial – Joanna Harnett – Evidence-Based Complementary and Alternative Medicine

Review: Links Between the Microbiome and Bone – Christopher J Hernandez – Journal of Bone and Mineral Research

Human vaginal microbiome

More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria – Sujatha Srinivasan – The Journal of Infectious Diseases

The Effects of Hormones and Vaginal Microflora on the Glycome of the Female Genital Tract: Cervical-Vaginal Fluid – Bernard J. Moncla – PLOS ONE

Review: New Systems for Studying Intercellular Interactions in Bacterial Vaginosis – Melissa M. Herbst-Kralovetz – The Journal of Infectious Diseases

Animal experiments

Lactulose differently modulates the composition of luminal and mucosal microbiota in C57BL/6J mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

American Ginseng Attenuates Colitis Associated Colon Carcinogenesis in Mice: Impact on Gut Microbiota and Metabolomics – Chong-Zhi Wang – Cancer Prevention Research

Alterations of Gut Microbiota After Roux-en-Y Gastric Bypass and Sleeve Gastrectomy in Sprague-Dawley Rats – Yikai Shao – Obesity Surgery

Animal microbiome

Diet diversity is associated with beta but not alpha diversity of pika gut microbiota – Huan Li – Frontiers in Mcrobiology

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats – Alejandra Hernandez-Agreda – mBio

Perspective: Hominid superorganisms – Julia A. Segre – Science

Plant, root, and soil microbiome

Long-term response of soil microbial communities to fire and fire-fighting chemicals –
A. Barreiro – Biology and Fertility of Soils

Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space – Varsik Martirosyan – Microbial Ecology

Lichen-associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude – Yanyan Wang – Frontiers in Microbiology

Water management impacts rice methylmercury and the soil microbiome – Sarah E. Rothenberg – Science of the Total Environment

Ecological restoration of a copper polluted vineyard: Long-term impact of farmland abandonment on soil bio-chemical properties and microbial communities – Luciano Cavani – Journal of Environmental Management

Review: Soil C and N models that integrate microbial diversity – Benjamin P. Louis – Environmental Chemistry Letters

Water and extremophile microbiome

Genomes of Abundant and Widespread Viruses from the Deep Ocean – Carolina Megumi Mizuno – mBio

Microbial communities associated with Antarctic snow pack and their biogeochemical implications – Runa Antony – Microbiological Research

Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats – André M. Comeau – Scientific Reports

Metabolomics

Review: Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health – Pamela Vernocchi – Frontiers in Microbiology

Functional foods

Review: Fermented Foods: Are They Tasty Medicines for Helicobacter pylori Associated Peptic Ulcer and Gastric Cancer? – Mydhily R. B. Nair – Frontiers in Microbiology

Bioinformatics

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF – Yingnan Cong – Scientific Reports
Exploring lateral genetic transfer among microbial genomes using TF-IDF – Yingnan Cong – Scientific Reports

Techniques

Design and Evaluation of Illumina MiSeq Compatible Primers for the 18S rRNA Gene for Improved Characterization of Mixed Microalgal Communities – Ian M. Bradley – Applied and Environmental Microbiology

More microbiology

Are multi-omics enough? – Cristina Vilanova – Nature Microbiology

Review: Bacterial Communities: Interactions to Scale – Reed M. Stubbendieck – Frontiers in Microbiology

The physiology and habitat of the last universal common ancestor – Madeline C. Weiss – Nature Microbiology

Press: Scientists find Luca, a single-cell, bacterium-like organism that is the common ancestor of all life on Earth – Andrew Griffin – Independent
Behold LUCA, the Last Universal Common Ancestor of Life on Earth – Jason Daley – Smithsonian
Our last common ancestor inhaled hydrogen from underwater volcanoes – Robert F. Service – Science
Meet Luca, the Ancestor of All Living Things – Nicholas Wade – New York Times

Microbes in the news

What your gut microbiome may be telling you – Katrina Clarke – The Record

Healthy microbiome supports antibiotic-free production – World Poultry

Charlottesville Lab to Test Microbiology of Local Breweries – NBC29

Nanostructured bacterial film makes new mortar resistant to water uptake – NanoWerk

Bik’s non-microbiology Picks

The Dutchies are still holding the top positions! A century of trends in adult human height – NCD Risk Factor Collaboration (NCD-RisC) – eLIFE

July 14, 2016

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Gut microbes and diabetes risk, llama sausages, urban greenness, and the sea turtle microbiome.

Pregnancy and birth

The Infant Gut Bacterial Microbiota and Risk of Pediatric Asthma and Allergic Diseases – Christine Cole Johnson – Translational Research

Human gut microbiome

Human gut microbes impact host serum metabolome and insulin sensitivity – Helle Krogh Pedersen – Nature

Press: Gut bacteria imbalance increases diabetes risk – EurekAlert
Gut bacteria imbalance increases diabetes risk – BioMed Central blog

Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial – Dorien Reijnders – Cell Metabolism

The Gut Microbiota from Lean and Obese Subjects Contribute Differently to the Fermentation of Arabinogalactan and Inulin – Marisol Aguirre – PLOS ONE

Review: The esophageal microbiota in health and disease – Vincenzo Di Pilato – Annals of the New York Academy of Sciences

Review: Colon microbiota fermentation of dietary prebiotics towards short-chain fatty acids and their roles as anti-inflammatory and antitumour agents: A review – Javier Fernández – Journal of Functional Foods

Animal and other experiments

Microbial Mat Functional and Compositional Sensitivity to Environmental Disturbance –
Eva Christine Preisner – bioRxiv

Gut microbiota directs PPARγ-driven reprogramming of the liver circadian clock by nutritional challenge – Mari Murakami – EMBO Reports

Preview: Microbially Produced Acetate: A “Missing Link” in Understanding Obesity? – Chad M. Trent – Cell Metabolism

Plant, root, and soil microbiome

Glyphosate and aminomethylphosphonic acid chronic risk assessment for soil biota – Georg von Mérey – Environmental Toxicology and Chemistry

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization – Mengxin Zhao – mSystems

Built environment microbiome

Urban greenness influences airborne bacterial community composition – Gwynne Mhuireach – Science of The Total Environment

Research Watch: Dirty environment for adult life: the bad, the good, the unknown – Jun Sun – Genes & Diseases

Food microbiology

Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity – Fontana Cecilia – International Journal of Food Microbiology

Metabolomics

Free eBook: Metabolomics – A Key Technology for Microbiome Research – Kirk Beebe – Metabolon

Techniques

Evaluation of VITEK matrix-assisted laser desorption ionization–time of flight mass spectrometry for identification of anaerobes – Zheng Xiao – Microbiology and Immunology

Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports

Rapid and Selective Detection of Pathogenic Bacteria in Bloodstream Infection with Aptamer-based Recognition – Haijing Shen – Applied Materials and Interfaces

Microbes in the news

Project to study sea turtle microbiomes in captivity and in the wild – Holly Ganz – MicroBEnet

Gonorrhea may soon become resistant to all antibiotics and untreatable – Helen Branswell – STAT news

Bacteriophage Therapy Grows as Alternative to Antibiotics – Michael McGrady – Heartland

Getting to the guts: Studying the gut microbiome to manage pain – Shay Stowell – Missouri State University

Career

Men cite themselves more than women do. The apparent trend has been on the rise over the past two decades – Dalmeet Singh Chawla – Nature

Bik’s non-microbiology Picks

A Gathering of Giants. A photographer slips into the ocean to swim among hundreds of sperm whales – witnessing a rarely seen social spectacle – Tony Wu – Biographic

The people who don’t get ‘Eleanor Rigby’. Happy music and sad sounds are not universal. – Nature

July 12, 2016

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Two papers on plant/root/soil microbiomes of interest, analysis of transcriptional regulatory networks, and too much non-prescription antibiotic use  in the US.

Human vaginal microbiome

Review: Bacterial vaginosis: a critical analysis of current knowledge – D Nasioudis – BJOG

Human gut microbiome

Gut microbiome analysis in neuromyelitis optica reveals over-abundance of Clostridium perfringens – Bruce A.C. Cree – Annals of Neurology

Review: Gut Microbiota and Intestinal Decolonization of Pathogenic Microorganisms – De-Chang Chen – Chinese Medical Journal

Animal experiments

Human Gut-Derived Prevotella histicola Suppresses Inflammatory Arthritis in Humanized Mice – Eric V. Marietta – Arthritis & Rheumatology

Press: Gut bacteria can cause, predict and prevent rheumatoid arthritis – Science Daily

Gastric Bypass Surgery Reverses Diabetic Phenotypes in Bdnf-Deficient Mice – Shujun Jiang – American Journal of Pathology

Press: New study suggests potential role for gut microbiota in diabetes remission after bypass surgery – News Medical

Plant, root, and soil microbiome

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant – Maggie R. Wagner – Nature Communications

Press: Breeding plants with more beneficial bacteria to feed the world won’t be simple, study says – Robin A. Smith – Phys.org

Soil inoculation steers restoration of terrestrial ecosystems – E. R. Jasper Wubs – Nature Plants

Soil microbes transplants could help restore damaged ecosystems – The dirt makes all the difference – Meaghan Lee Callaghan – PopSci

Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil – Nicole K. Scharko – Environmental Science & Technology

Opinion: Plant microbiota affects seed transmission of phytopathogenic microorganisms – Matthieu Barret – Molecular Plant Pathology

Metagenomics and bioinformatics

A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data – Elizabeth T. Hobbs – Algorithms for Molecular Biology

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles – Cuncong Zhong – PLOS Computational Biology

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights – Edoardo Pasolli – PLOS Computational Biology

Review: Metagenome-wide association studies: fine-mining the microbiome – Jun Wang – Nature Reviews Microbiology

Proteomics

An alignment-free ‘metapeptide’ strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing – Damon H. May – Journal of Proteome Research

Bioreactor microbiology

A light-induced shortcut in the planktonic microbial loop – Robert Ptacnik – Scientific Reports

More microbiology

Non-prescription antimicrobial use in a primary care population in the United States: evidence for action – Roger Zoorob – Antimicrobial Agents and Chemotherapy

Press: Self-prescribing antibiotics is a big problem – American Society for Microbiology – EurekAlert

Transfer of DNA from Bacteria to Eukaryotes – Benoît Lacroix – mBio

Origins of pandemic clones from environmental gene pools – B. Jesse Shapiro – bioRxiv

UTSA professor’s study describes new strategies for investigating microbial outbreaks – EurekAlert

Microbes in the news

Railroad spanning Great Salt Lake helps MSU scientists understand origins of reef-like structures – Skip Anderson – Montana State University

The colon is defended from bacteria by a self-sacrificing sentinel cell – EurekAlert