Category Archives: Metagenomics & Bioinformatics

August 9, 2016

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Climate change and increasing Vibrio species in North Atlantic, microbiome of the aging mouth, Antarctic soil around Little Auk colony.

Events

5th Exploring Human Host-Microbiome Interactions in Health and Disease – Welcome Genome Campus, Cambridge, UK, 7-9 September 2016

4th World Congress on Targeting Microbiota – Institut Pasteur, France, October 17-19, 2016

Hot topics in microbiology: Campden BRI conference – Campden BRI, Chipping Campden, Gloucestershire, UK, October 13-14

Today & tomorrow – live webcast – Standards for Microbiome Measurements @NIST – Jonathan Eisen – MicroBEnet

General microbiome

Note: includes 16S rRNA gene studies as well, so not metagenomic sensu stricto: An overview of major metagenomic studies on human microbiomes in health and disease – Hongfei Cui – Quantitative Biology

Brazil: A Step Forward to Empower Global Microbiome Research Through Local Leadership – Victor S. Pylro – Trends in Microbiology

Human oral microbiome

Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms – Takahiko Shiba – Scientific Reports

Oral microbial community typing of caries and pigment in primary dentition – Yanhui Li – BMC Genomics

Review: The subgingival periodontal microbiota of the aging mouth – Magda Feres – Periodonotology 2000

Human respiratory microbiome

Review: The microbiome in chronic inflammatory airway disease: A threatened species – Robin John Green – The South African Medical Journal

Review: Lung microbiome in human immunodeficiency virus infection – Homer L. Twigg IIIa – Translational Research

Human vaginal microbiome

Evaluation of the vaginal flora in pregnant women receiving opioid maintenance therapy: a matched case-control study – Alex Farr – BMC Pregnancy Childbirth

Human gut microbiome

Microbial Factors Associated with Postoperative Crohn’s Disease Recurrence – Emily K. Wright – Journal of Crohn’s and Colitis

The mucosal microbiota in a young child with severe non-Helicobacter gastritis – Geoffrey A. Preidis – Therapeutic Advances in Gastroenterology

Profile of Gut Microbiota Associated With the Presence of Hepatocellular Cancer in Patients With Liver Cirrhosis – M. Grąt – Transplantation Proceedings

Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population – Akira Andoh – Journal of Clinical Biochemistry and Nutrition

Book Chapter: The Second Brain and Possible Interactions with the Heart – Rosa Sollazzo – Psychotherapy for Ischemic Heart Disease

Infection microbiology

Comparison of methods for the identification of microorganisms isolated from blood cultures – Aydir Cecília Marinho Monteiro – Annals of Clinical Microbiology and Antimicrobials

Animal experiments

Disturbance in the Mucosa-Associated Commensal Bacteria Is Associated with the Exacerbation of Chronic Colitis by Repeated Psychological Stress; Is That the New Target of Probiotics? – Sohei Arase – PLOS ONE

Role of the Gut Microbiome in Modulating Arthritis Progression in Mice – Xiaofei Liu – Scientific Reports

Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut – Thibault G. Sana – PNAS

Animal microbiome

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards – Tiantian Ren – Molecular Ecology

The gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles – Aileen Berasategui – Molecular Ecology

Plant, root, and soil microbiome

The Arctic soil bacterial communities in the vicinity of a little auk colony – Sylwia Zielinska – Frontiers in Microbiology

Soil Fungal:Bacterial Ratios Are Linked to Altered Carbon Cycling – Ashish A. Malik – Frontiers in Microbiology

Ancient landscapes and the relationship with microbial nitrification – Sasha N. Jenkins – Scientific Reports

Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons – David W. Cleary – FEMS Microbiology Ecology

Are Epiphytic Microbial Communities in the Carposphere of Ripening Grape Clusters (Vitis vinifera L.) Different between Conventional, Organic, and Biodynamic Grapes? – Elizabeth Kecskeméti – PLOS ONE

Bacterial communities in Antarctic lichens – Chae Haeng Park – Antarctic Science

Water and extremophile microbiome

Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic – Luigi Vezzulli – PNAS

Press: We’re trashing the oceans — and they’re returning the favor by making us sick – Chris Mooney – The Washington Post
Deadly Bacteria Spread across Oceans as Water Temperatures Rise. Cholera bacteria and others arise in more places and in greater abundance – Umair Irfan – Scientific American
Warming seas linked to rise in cholera bacteria in Europe and US – Brian Owens – New Scientist

Microbial community structure in hypolentic zones of a brine lake in a desert plateau, China – Wenzhen Yuan – Environmental Earth Sciences

Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts) of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile – Ana B. Fernandez – Frontiers in Microbiology

Bioreactor microbiome

The full-scale anaerobic digestion microbiome is represented by specific marker populations – Jo De Vrieze – Water Research

Viruses and phages

Challenges in the analysis of viral metagenomes – Rebecca Rose – Virus Evolution

Metagenomics and bioinformatics

Bipartite graph analyses reveal inter-domain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins – Alexander L. Jaffe – Environmental Microbiology

FARAO – The Flexible All-Round Annotation Organizer – Rickard Hammarén – Bioinformatics

Identifying wrong assemblies in de novo short read primary sequence assembly contigs – Vandna Chawla – Journal of Biosciences

A Bayesian Framework for the Classification of Microbial Gene Activity States – Craig Disselkoen – Frontiers in Microbiology

Techniques

Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs – Martin A. Fischer – Frontiers in Microbiology

More microbiology

Editorial: New insights into microbial ecology through subtle nucleotide variation – A M. Eren – Frontiers in Microbiology

Neisseria meningitides Can Survive in Corpses for At Least Eleven Days – Antonio Osculati – Frontiers in Cellular and Infection Microbiology

Microbes in the news

List of papers about bias in microbiome techniques: The unbearable madness of microbiome – Mick Watson – Opiniomics

Book Review: Follow your gut – The Enormous Impact of Tiny Microbes – Daniel K. Morais – Frontiers in Microbiology

Brito went to Fiji to study mobile genes in human microbiome – Tom Fleischman – Cornell Chronicle

MSU graduate awarded NSF fellowship to study disease affecting world’s citrus crops – Denise Hoepfner – Montana State University

Bacteria Could Aid Search for Creatures On Other Planets – Elizabeth Howell – Astrobiology Magazine

U.Va. scientists make important discovery about dangerous bacteria strains
Researchers pinpoint mechanisms of C. difficile strains – Daisy Xu – Cavalier Daily

Did farming practices in China create an antibiotic resistant bacteria that’s spreading around the world? – Alanna Shaikh – United Nations Dispatch

Science, publishing, and career

Dog eat dog: is a troubled expedition to Kenya causing the Smithsonian to devour its young?
A star scientist stands accused of misconduct, but colleagues say he’s being railroaded
– Michael Balter – The Verge

A “Scientific Diversity” Intervention to Reduce Gender Bias in a Sample of Life Scientists – Corinne A. Moss-Racusin – CBE Life Sciences Education

Bik’s non-microbiology Picks

Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children – Michelle M. Stein – New England Journal of Medicine

August 6, 2016

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Airwair microbiome at birth, fungi on strawberries, molds in a library.

Pregnancy and birth

The Airway Microbiome at Birth – Charitharth Vivek Lal – Scientific Reports

Press: Discovery of Infants’ Airway Microbiomes May Help Predict Lung Disease
A newborn’s airway — once thought to be sterile until after birth — is colonized by bacteria– University of Alabama at Birmingham
Discovery of infants’ airway microbiomes may help predict lung disease – Jeff Hansen – Medical Xpress

Gestational Diabetes is associated with changes in Placental Microbiota and Microbiome – Judit Bassols – Pediatric Research

Human respiratory microbiome (also see Pregnancy and Birth)

Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features – Guoqin Yu – Genome Biology

High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors – Daniela Janek – PLOS Pathogens

Human ear microbiome

Molecular microbiological profile of chronic suppurative otitis media – Michel Neeff – Journal of Clinical Microbiology

Human gut microbiome

Antibiotic-Induced Gut Microbiota Disruption Decreases TNF-α Release by Mononuclear Cells in Healthy Adults – Jacqueline M. Lankelma – Clinical and Translational Gastroenterology

Review: Fecal Microbiota Transplantation and Its Usage in Neuropsychiatric Disorders – Alper Evrensel – Clinical Psychopharmacology and Neuroscience

Review: Interactions between the gut microbiome and the central nervous system and their role in schizophrenia, bipolar disorder and depression – Adrian Andrzej Chrobak – Archives of Psychiatry and Psychotherapy

Animal microbiome

Strain diversity and host specificity in a specialized gut symbiont of honey bees and bumble bees – J. Elijah Powell – Molecular Ecology

Flow cytometric enumeration of bacterial in the coral surface mucus layer – Yvan Bettarel – Journal of Microbiological Methods

Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank – Tanya Brown – PeerJ Preprint

Plant, root, and soil microbiome

Metagenomic Analysis of Fungal Diversity on Strawberry Plants and the Effect of Management Practices on the Fungal Community Structure of Aerial Organs – Ahmed Abdelfattah – PLOS ONE

The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon-availability in Mediterranean semiarid soils – Felipe Bastida – Molecular Ecology

Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem – Allison M. Veach – Molecular Ecology

Review: Phytoremediation: state-of-the-art and a key role for the plant microbiome in future trends and research prospects – Sofie Thijs – International Journal of Phytoremediation

Review: Bacterial pathogenesis of plants: future challenges from a microbial perspective. Challenges in Bacterial Molecular Plant Pathology – Sebastian Pfeilmeier – Molecular Plant Pathology

Review: Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments – Lucie Musilova – Int J Mol Sci

Water and extremophile microbiome

Unexpected biodiversity of ciliates in marine samples from below the photic zone – Jean-David Grattepanche – Molecular Ecology

Meltwater export of prokaryotic cells from the Greenland Ice Sheet – Karen A. Cameron – Environmental Microbiology

Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas – Haixia Zhou – Frontiers in MIcrobiology

Review: Extremophilic adaptations and biotechnological applications in diverse environments – James Charlesworth – AIMS Microbiology

Built environment microbiome

Detection of volatile metabolites of moulds isolated from a contaminated library – Anna Micheluz – Journal of Microbiological Methods

Review: Shoe soles as a potential vector for pathogen transmission: A systematic review – Tasnuva Rashid – Journal of Applied Microbiology

Bioinformatics and metagenomics
PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories – Victor Hanson-Smith – PLOS Computational BIology

The Phylogenetic LASSO and the Microbiome – Stephen T Rush – arXiv

Microbiome networks: A systems framework for identifying candidate microbial assemblages for disease management – Ravin Poudel – Phytopathology

Techniques

On the study of microbial transcriptomes using second- and third-generation sequencing technologies – Sang Chul Choi – Journal of Microbiology

Microbes in the news

Notre Dame Researcher Explores Bacteria beyond the Ability of Typical Hospital Setting: Gail Weaver – Nina Welding – Engineering

 

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 4, 2016

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Human breast tissue microbes, foliar bacteria, SAR11 genomes, and a new book about babies growing up too clean.

Human oral microbiome

Oral, Intestinal, and Skin Bacteria in Ventral Hernia Mesh Implants – Odd Langbach – Journal of Oral Microbiology

A novel compound to maintain a healthy oral plaque ecology in vitro – Marleen M. Janus
– Journal of Oral Microbiology

Paper on periodontal disease by computer scientists, but no dentists involved, and no mentioning of ethics approval or informed consent…
Metagenomic Analysis and Features Selection in Human Oral Microbiota Associated with Periodontal Disease – Wen-Pei Chen – The 33rd Workshop on Combinatorial Mathematics and Computation Theory

Human skin/breast tissue microbiology

The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease – Tina J. Hieken – Scientific Reports

Press: Researchers identify breast microbiome/bacterial differences between healthy and cancerous tissue – Medical Xpress

Also contains animal experiments: Transplantation of human skin microbiota in models of atopic dermatitis – Ian A. Myles – JCI Insight

Human gut microbiome

Effects of scFOS on the composition of fecal microbiota and anxiety in patients with irritable bowel syndrome: a randomized, double blind, placebo controlled study – F. Azpiroz – Neurogastroenterology & Motility

Letter: Dyspepsia and the microbiome: time to focus on the small intestine – Laurie Zhong – Gut

Review: Exposure to inorganic arsenic can lead to gut microbe perturbations and hepatocellular carcinoma – Jonathan Choiniere – Acta Pharmaceutica Sinica B

Review: Modulation of type 1 and type 2 diabetes risk by the intestinal microbiome –
Alexandra Paun – Pediatric Diabetes

Animal experiments

Pterostilbene-induced changes in gut microbiota composition in relation to obesity – Usune Etxeberria – Molecular Nutrition & Food Research

The skin microbiome in allergen-induced canine atopic dermatitis – Felipe Pierezan – Veterinary Dermatology

Plant, root, and soil microbiome

Foliar bacteria and soil fertility mediate seedling performance: a new and cryptic dimension of niche differentiation – Eric A. Griffin – Ecology

DGGE: Effect of karst rocky desertification on soil fungal communities in Southwest China – P.C. Wang – Genetics and Molecular Research

Water and extremophile microbiome

SAR11 bacteria linked to ocean anoxia and nitrogen loss – Despina Tsementzi – Nature

Press: Global warming, a dead zone and surprising bacteria – Phys.org

Sulfate reduction and inorganic carbon assimilation in acidic thermal springs of the Kamchatka peninsula – E. N. Frolov – Microbiology

Book Chapter: Bacterial Diversity of the Boka Kotorska Bay – Sandra Jokanović – The Handbook of Environmental Chemistry

Bioinformatics and metagenomics

An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria – Stephen Nayfach – bioRxiv

Advances in the recovery of haplotypes from the metagenome – Samuel M Nicholls – bioRxiv

Techniques

Virtual microfluidics for digital quantification and single-cell sequencing – Liyi Xu – Nature Methods

Microbial Nanoculture as an Artificial Microniche – Tagbo H. R. Niepa – Scientific Reports

Considerations for optimizing microbiome analysis using a marker gene – Jacobo de la Cuesta-Zuluaga – Frontiers in Nutrition

Microbes in the news

Dirty baby: Just how clean does your child need to be? – Bill Daley – Chicago Tribune

New book: Let Them Eat Dirt. Saving Your Child From an Oversanitized World – B. Brett Finlay and Marie-Claire Arrieta

Cloud computing used to analyze microbiological samples – Tim Sandle – Digital Journal

Bacteria Show Capacity for Rapid, Beneficial Mutations – University of Texas News

Video: Vibrio cholerae swimming in the gut of a live zebrafish – Phys.org

How the microbiome will lead a revolution in the consumerization of personalized medicine and diet – Kobi Gershoni – Tech Crunch
Science, publishing, and career

Scholarly Olympics: How the games have shaped research. A graphical guide to the impact of the Olympics on science – Ramin Skibba – Nature

‘Kudos’ promises to help scientists promote their papers to new audiences
Increasingly popular social-media tool says it can maximize reach and impact of research – Jeffrey Perkel – Nature

August 3, 2016

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Saliva and Polycystic Ovary Syndrome, early colonization of honey bees, hospital air metagenomes, analysis tool for viral metagenomes.

Human oral microbiome

The Salivary Microbiome in Polycystic Ovary Syndrome (PCOS) and its Association with Disease-related Parameters: A Pilot Study – Lisa Lindheim – Frontiers in Microbiology

A novel compound to maintain a healthy oral plaque ecology in vitro – Marleen M. Janus – Journal of Oral Microbiology

Human vaginal microbiome

Does the vaginal microbiota plays a role in the development of cervical cancer? – Maria Kyrgiou – Translational Research

Human skin microbiome

Diverse human skin fungal communities in children converge in adulthood – Jay-Hyun Jo – Journal of Investigative Dermatology

Human gut microbiome

A pleiotropic missense variant in SLC39A8 is associated with Crohn’s disease and human gut microbiome composition – Dalin Li – Gastroenterology

Press: Genetic Variant Newly Linked to Crohn’s Disease Also Associated with Altered Gut Microbiome Composition – PR Web

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Review: A clinical update on the significance of the gut microbiota in systemic autoimmunity – Elizabeth C. Rosser – Journal of Autoimmunity

Review: The human gut microbiome of Latin America populations: a landscape to be discovered – Fabien Magne – Current Opinion in Infectious Diseases

Animal microbiome

Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers – Ryan S. Schwarz – PNAS

Another pika paper by the same authors (who killed all pika to obtain gut contents – booh): Pika gut may select for rare but diverse environmental bacteria – Huan Li – Frontiers in Microbiology

Review: Bacterial symbiosis in the fish gut and its role in health and metabolism – Goutam Banerjee – Symbiosis

Plant, root, and soil microbiome

Diverse gene functions in a soil mobilome – Wenting Luo – Soil Biology and Biochemistry

Genetic Diversity and Association Characters of Bacteria Isolated from Arbuscular Mycorrhizal Fungal Spore Walls – Gopal Selvakumar – PLOS ONE

Spatio-temporal variation of core and satellite arbuscular mycorrhizal fungus communities in Miscanthus giganteus – Christopher J. Barnes – Frontiers in Microbiology

DGGE: Impacts of Grazing Intensity and Plant Community Composition on Soil Bacterial Community Diversity in a Steppe Grassland – Tong-bao Qu – PLOS ONE

Book chapter: Calling in the Dark: The Role of Volatiles for Communication in the Rhizosphere – Nicole M. van Dam – Deciphering Chemical Language of Plant Communication

Book Chapter: Truffle-Associated Bacteria: Extrapolation from Diversity to Function – Elena Barbieri – True Truffle (Tuber spp.) in the World

Water and extremophile microbiome

Yeasts from sub-Antarctic region: biodiversity, enzymatic activities and their potential as oleaginous microorganisms – A. Martinez – Extremophiles

First report of microorganisms of Caucasus glaciers (Georgia) – Nicoletta Makowska – Biologia

Species sorting along a subsidy gradient alters bacterial community stability – Mario E. Muscarella – Ecology

Air microbiome / Built environment microbiome

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes – Paula King – PLOS ONE

Bioinformatics

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies – Martin Norling – PLOS ONE

MetaCoMET: a web platform for discovery and visualization of the core microbiome – Yi Wang – Bioinformatics

More microbiology

Tempo and mode of genome evolution in a 50,000-generation experiment – Olivier Tenaillon – Nature

Press: Still changing after all these years. Long-term evolution experiment looks at genetic changes in bacteria: Richard Lenski – Science Daily

Review: Survival of the Fittest: How Bacterial Pathogens Utilize Bile To Enhance Infection – Jeticia R. Sistrunk – Clinical Microbiology Reviews

Book: Infective Endocarditis. Epidemiology, Diagnosis, Imaging, Therapy, and Prevention – Editors: Gilbert Habib – Springer

Élie Metchnikoff (1845–1916): celebrating 100 years of cellular immunology and beyond – David M. Underhill – Nature Reviews Immunology

Microbes in the news

Understanding diverse microbial communities: An interview with A. Murat Eren (Meren) – Kelle Freel – The Molecular Ecologist

Back from vacation? Your gut bacteria picked up souvenirs, too – Meredith Knight – Genetic Literacy Project

Evelo, Mayo Clinic team up to use bacteria for cancer immunotherapies – Ben Adams – Fierce Biotech

Plop into Canada’s first poop-themed dessert café next month – Heather Dockray – Mashable
Poop Dessert Cafe to open in Koreatown.Toronto is poised to get its first poop-themed café, set to open in August – The Star
First poo-themed dessert cafe set to open in Canada – Rachael Revesz – The Independent

Council agrees to trial of microbiology treatment – Lici Beveridge – Hattiesburg American

Opinion: Goals and possibilities in microbiology – Andrea Taboada – The Independent Florida Alligator

How Do Microbes Build Resistance to Metals? – Contagion

Bacteria Needed To Save Coral Reef – The Munich Eye

WATCH: Pac-Man Faithfully Recreated with Microbes – Nathaniel Scharping – Discover Magazine

 

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 30, 2016

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Honey bee gut microbiome altered by pesticides, colobine primates, sulfur vents, bioaerosol, failed microbiome spore transplant trial.

Events

London Microbiome Workshop – September 7th 2016, Royal College of Physicians, London

Pregnancy and birth

Antibiotic perturbation of the preterm infant gut microbiome and resistome – Andrew J. Gasparrini – Gut Microbes

Multisite microbiome

Acquisition of a high diversity of bacteria during Hajj pilgrimage, including Acinetobacter baumannii with blaOXA-72, and Escherichia coli with blaNDM-5 carbapenemases – Thongpan Leangapichart – Antimicrobial Agents and Chemotherapy

Human gut microbiome

Limited prolonged effects of rifaximin treatment on irritable bowel syndrome-related differences in the fecal microbiome and metabolome – Natalia Zeber-Lubecka –
Gut Microbes

Altered gut microbiota in Rett syndrome – Francesco Strati – Microbiome

Animal experiments

Honey bee gut microbiome is altered by in-hive pesticide exposures – Madhavi Kakumanu – Frontiers in Microbiology

Animal microbiome

The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome – Hang Wang – The ISME Journal

Using the gut microbiota as a novel tool for examining colobine primate GI health – Katherine R. Amato – Global Ecology and Conservation

Plant, root, and soil microbiome

Bioprospecting metagenomics of a microbial community on cotton degradation: mining for new glycoside hydrolases – Guoxiu Zhang – Journal of Biotechnology

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain – Congcong Shen – Frontiers in Microbiology

Review: Plant litter decomposition: drivers insight to the ecological process – Gaurav Mishra – European Journal of Biological Research

Water and extremophile microbiome

Transcriptional control in marine copiotrophic and oligotrophic bacteria with streamlined genomes – Matthew T. Cottrell – Applied and Environmental Microbiology

Distribution and niche separation of planktonic microbial communities in the water columns from the surface to the hadal waters of the Japan Trench under the eutrophic ocean – Takuro Nunoura – Frontiers in Microbiology

Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area – Neng Fei Wang – Frontiers in Microbiology

Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA – Priscilla J. Miranda – Frontiers in Microbiology

Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents – Begüm D. Topçuoğlu – Frontiers in Microbiology

Review: Halophiles: Champions of Environmental Adaptations and Their Industrial Applications – Rachana Singh – Current Biological Engineering (WTF: $63.00)

Review: An overview of siderophores for iron acquisition in microorganisms living in the extreme – Luis O. De Serrano – BioMetals

Air microbiome

Review: Approach of molecular methods for the detection and monitoring of microbial communities in bioaerosols: A review – Keunje Yoo – Journal of Environmental Sciences

Oil reservoir microbiome

Species divergence vs functional convergence characterizes crude oil microbial community assembly – Yong Nie – Frontiers in Microbiology

Metagenomics

Editorial: From Genes to Species: Novel Insights from Metagenomics – Eamonn P. Culligan – Frontiers in Microbiology

Sequencing techniques

Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing – Minh Duc Cao – GigaScience

Microbes in the news

Poop Pill’s Surprise Failure Shows That the Microbiome is Still a Mystery – Ryan Cross – MIT Technology Review
Gut check: Seres Therapeutics shares plunge after microbiome drug fails in trial – CNBC
Seres Therapeutics Announces Interim Results from SER-109 Phase 2 ECOSPOR Study in Multiply Recurrent Clostridium Difficile Infection – Seres

I, microbe: Book Review of “I Contain Multitudes” by Ed Yong – Silvia Bulgheresi – Nature Microbiology
Hot off the press: Interview with Ed Yong – Andrew Jermy – Nature Microbiology

Teasing out the microbiome of the Kansas prairie. One teaspoonful of soil holds DNA of tens of thousands of microbial species – EurekAlert
Teasing out the microbiome of the Kansas prairie. One teaspoonful of soil holds DNA of tens of thousands of microbial species – Science Daily

Parasitic infection may have spoiled zebrafish experiments.Common contaminant may change shoaling behaviour, a proxy for stress and anxiety in behavioural studies. – Petra Szilagyi – Nature
What Does Your Poop Say About Your Evolution, and Other Ecological Connections to the Microbiome – Jens Hegg – PLOS Blogs

Powerful new bacteria discovered in Cookeville hot tub – Daily News Journal

Could a new CREAM fight off superbugs? Scientists develop lotion which stops bacteria getting into wounds – Madlen Davies – Daily Mail

There’s Nothing Green About Jill Stein’s Vaccine Stance – Emily Willingham – Forbes

Your soap and toothpaste could be messing with your microbiome – Alison Moodie – The Guardian

Anthrax sickens 13 in western Siberia, and a thawed-out reindeer corpse may be to blame – Ben Guarino – Washington Post

Bik’s not-microbiology Picks

Khloe Kardashian’s Vagina Oil Is a Bad Idea. Koko is telling her young female followers to moisturize their ‘vaginal lining’ with Vitamin E. Definitely do not do this– Samantha Allen – The Daily Beast

The Physicians Committee Releases Seven Dietary Guidelines for a Healthy Microbiota
The Key to Optimal Gut Health? Eat 50 to 55 Grams of Daily Fiber – PCRM

 

July 29, 2016

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Bifidobacteria/Spirochaetes trade-off in Italians vs. Hadza, asthma, transferring depression with human stool to rats, sea squirts symbionts, spacial structure of biofilms, and a glowing review of Ed Yong’s book “I Contain Multitudes”.

General microbiome

Dysbiosis Across Multiple Body Sites in Critically Ill Adult Surgical Patients – Andrew Yeh – Shock

Pregnancy / human oral microbiome

Smoking, pregnancy and the subgingival microbiome – Akshay D. Paropkari – Scientific Reports

Review: An Integrated Review of Intestinal Microbiota in the Very Premature Infant – Melissa C. Dollings –  Neonatal Network

Human respiratory microbiome

Bacterial microbiota of the upper respiratory tract and childhood asthma – Martin Depner – Journal of Allergy and Clinical Immunology

Review: The role of anaerobic bacteria in the cystic fibrosis airway – Laura J. Sherrard – Current Opinion in Pulmonary Medicine

Human vaginal microbiome

Commentary: The relationship between the vaginal microbiome and human health – MR Millar – BJOG

Human gut microbiome

Variations in the Post-weaning Human Gut Metagenome Profile As Result of Bifidobacterium Acquisition in the Western Microbiome – Matteo Soverini – Frontiers in Microbiology

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations – Alessandra Riva – Environmental Microbiology

Histamine-secreting microbes are increased in the gut of adult asthma patients – Weronika Barcik – Journal of Allergy and Clinical Immunology

Dietary Supplementation with Rice Bran or Navy Bean Alters Gut Bacterial Metabolism in Colorectal Cancer Survivors – Amy M. Sheflin – Molecular Nutrition & Food Research

Four-week consumption of a Bifidobacterium bifidum strain modulates dominant intestinal bacterial taxa and fecal butyrate in healthy adults – Giorgio Gargari – Applied and Environmental Microbiology

Fecal microbiota transplantation for patients with steroid-resistant/dependent acute graft-versus-host disease of the gut – Kazuhiko Kakihana – Blood

Trial: Effect of prebiotic intake on gut microbiota, intestinal permeability and glycemic control in children with type 1 diabetes: study protocol for a randomized controlled trial – Josephine Ho – Trials

Opinion: How stable is the human gut microbiota? And why this question matters – Harald Brüssow – Environmental Microbiology

Research highlight: Microbial mobilomes differ between societies – Naomi Attar – Nature Reviews Microbiology

Review: High-Resolution Characterization of the Human Microbiome – Cecilia Noecker – Translational Research

Review: Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases – Mingming Sun – Journal of Gastroenterology

Review: The influence of gut derived CD39 regulatory T cells in CNS demyelinating disease – Javier Ochoa-Repáraz – Translational Research

Review: Fecal microbiota transplantation in inflammatory bowel disease: the quest for the holy grail – B Pigneur – Mucosal Immunology

Review: The Gut Microbiota in Immune-Mediated Inflammatory Diseases – Jessica D. Forbes – Frontiers in Microbiology

Review: Regulation of Autoimmunity by the Microbiome – Carlos R. Zárate-Bladés – DNA and Cell Biology

Animal experiments

Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat – John R. Kelly – Journal of Psychiatric Research

The microbiota contributes to CD8+ T cell activation and nutrient malabsorption following intestinal infection with Giardia – Infection and Immunity – Aleksander Keselman

Gut Microbial Membership Modulates CD4 T Cell Reconstitution and Function after Sepsis – Javier Cabrera-Perez – Journal of Immunology

Metabolite exchange within the microbiome produces compounds that influence Drosophila behavior – Caleb N. Fischer – bioRxiv

Variation in the Gut Microbiota of Termites (Tsaitermes ampliceps) Against Different Diets – Lijuan Su – Applied Biochemistry and Biotechnology

Animal microbiome

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts – Lars Schreiber – Frontiers in Microbiology

Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material – Ali H.D. Janab -Journal of Microbiological Methods

Death Becomes Them: Bacterial community dynamics and stilbene antibiotic production in Galleria mellonella cadavers killed by Heterorhabditis/Photorhabdus – Amanda C. Wollenberg – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium – German Zafra – Journal of Hazardous Materials

Water and extremophile microbiome

Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale – Amit Vikram – Microbial Ecology

Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods – Vinh D. Pham – Environmental Microbiology

Protocol: Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME – Matthieu Leray – Marine Genomics

Protocol: Sampling of Riverine or Marine Bacterial Communities in Remote Locations: From Field to Publication – Katja Lehmann – Marine Genomics

Microbes in space

Assessment of the Forward Contamination Risk of Mars by Clean Room Isolates from Space-Craft Assembly Facilities through Aeolian Transport – a Model Study – Luc van Heereveld – Origins of Life and Evolution of Biospheres

Built environment microbiome

Figures appear to show a gradual change, not a break, but: Summer holidays as break-point in shaping a tannery sludge microbial community around a stable core microbiota – Cesira Giordano – Scientific Reports

Food microbiology

Detailed analyses of the bacterial populations in processed cocoa beans of different geographic origin, subject to varied fermentation conditions – Cristian Bortolini – International Journal of Food Microbiology

Bioinformatics and metagenomics

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets – Scott C. Ritchie – Cell Systems

Techniques

The effect of DNA extraction methodology on gut microbiota research applications – Konstantinos Gerasimidis – BMC Research Notes

Biofilms

Review: Spatial structure, cooperation and competition in biofilms – Carey D. Nadell – Nature Reviews Microbiology

Microbes in the news

A glowing book review: Living in a microbial world, book review of “I Contain Multitudes The Microbes Within Us and a Grander View of Life” by Ed Yong – Susan Perkins – Science

State College of Florida, New College graduate wins microbiology award: Stephanie Morgan’s research won an award at the Small World Initiative Symposium – Bradenton Herald

Microbiology: A budding researcher creates a stir with her LIST-supported project: Camilla Hurst – Luxembourg Institute of Science And Technology (LIST)

‘Bugs’ on the subway: Monitoring the microbial environment to improve public health – Harvard

‘Nose-y’ Bacteria Could Yield A New Way To Fight Infection – Carolyn Beans – NPR

The Marine Microbiome – A treasure trove of scientific and industrial potential – Cordis Europa
Video: Revealing the Secrets of Marine Microbes: methods that are being used to isolate and culture marine microorganisms – MaCuMBA project

July 28, 2016

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Maternal HIV status and infant microbiome development, nose bacteria producing antibiotics, gases produced by gut microbes, microbial mats in Hawaiian lava caves.

Pregnancy and birth

Maternal HIV infection influences the microbiome of HIV-uninfected infants – Jeffrey M. Bender – Science Translational Medicine

Press: Maternal HIV status may disrupt normal microbiome development in uninfected infants – Medical Xpress

Human respiratory microbiome

Human commensals producing a novel antibiotic impair pathogen colonization – Alexander Zipperer – Nature

Press: Scientists are looking everywhere, and we mean everywhere, for new antibiotics – Katherine Ellen Foley – Quartz
Nose-Dwelling Bacteria Could Be Antibiotic Factories, Study Says – Robert Lee Hotz – Wall Street Journal

Human vaginal microbiome

Desialylation of Neisseria gonorrhoeae Lipooligosaccharide by Cervicovaginal Microbiome Sialidases: The Potential for Enhancing Infectivity in Men – Margaret R. Ketterer – Journal of Infectious Diseases

Does the cervicovaginal microbiome facilitate transmission of Neisseria gonorrhoeae from women to men? Implications for understanding transmission of gonorrhea and advancing vaccine development – William M. Shafer – Journal of Infectious Diseases

Human gut microbiome

Review: Neuromodulatory effects and targets of the SCFAs and gasotransmitters produced by the human symbiotic microbiota –  Alexander V. Oleskin – Microbial Ecology in Health and Disease

Press: Explosive new findings: Farting shown to play a role in regulating your brain and behavior – Kelly Hodgkins – Yahoo Tech

Review: Progress in Our Understanding of the Gut Microbiome: Implications for the Clinician – Sara Iqbal – Current Gastroenterology Reports

 
Animal microbiome

Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous-collared sparrows – Camilo Escallón – Functional Ecology

Review: The rich somatic life of Wolbachia – Jose E. Pietri – MicrobiologyOpen

Plant, root, and soil microbiome

Diversity of root-associated arbuscular mycorrhizal fungal communities in a rubber tree plantation chronosequence in Northeast Thailand – Laetitia Herrmann – Mycorrhiza

Bromeliad tanks are unique habitats for microbial communities involved in methane turnover – Franziska B. Brandt – Plant and Soil

Soil compartment is a major determinant of the impact of simulated rainfall on desert microbiota – Shazia N. Aslam – Environmental Microbiology

Assessing Fungal Population in Soil Planted with Cry1Ac and CPTI Transgenic Cotton and Its Conventional Parental Line Using 18S and ITS rDNA Sequences over Four Seasons – Xiemin Qi – Frontiers in Plant Science

Systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization – Daniel B. Müller – Molecular and Cellular Proteomics

Water and extremophile microbiome

(PDF) Microbial mat communities in Hawaiian lava caves – Michael N. Spilde – International Symposium on Vulcanospeleology

Poster, abstract only: Microbial Diversity of Culinary Salts – Galen Muske – Utah Space Grant Consortium

Built environment microbiome

Influence of carbon sources and concrete on microbially induced corrosion of carbon steel in subterranean groundwater environment – Pauliina Rajala – Corrosion

Bioinformatics and metagenomics

MBMC: An Effective Markov Chain Approach for Binning Metagenomic Reads from Environmental Shotgun Sequencing Projects – Wang Ying – OMICS: A Journal of Integrative Biology

Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations – Aaron Y. Lee – BMC Bioinformatics

Review: Computational Biology in the 21st Century: Scaling with Compressive Algorithms – Bonnie Berger – Communications of the ACM

Microbes in the news

Five new studies will examine how the trillions of tiny organisms that call our bodies home can impact health – University at Buffalo

NASA releases ‘Microbiomics: The Living World In and On You’ – Video highlights Twins Study microbiome investigation – EurekAlert

The Olympians can leave. Brazil’s poor live with filthy, reeking water every day – Melissa Bailey – STAT News

Bizarre bacteria causing major cattle disease named by researchers – Pajaroellobacter abortibovis causes “foothill abortion disease” –  Science Daily

Bik’s non-microbiology Picks

From Impossible Foods, co-founded by Patrick Brown, a former Stanford professor: Impossible burger: New York’s latest food craze is a veggie burger that bleeds – Amanda Holpuch – The Guardian

July 27, 2016

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Gut microbiome in men with pelvic pain, zebrafish stomach motility and bacterial competition, microbiomes of indoor environments, and the Microbial Olympics.

Human gut microbiome

Analysis of Gut Microbiome Reveals Significant Differences between Men with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls – Daniel A. Shoskes – Journal of Urology

Press: Gut Microbiome Diversity Lower in Chronic Pelvic Pain Syndrome – Medical Xpress

Animal and bioreactor experiments

Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota – Travis J Wiles – PLOS Biology

Press: Real-time imaging of fish gut ties bacterial competition to gut movements – Science Daily

Microbial Communities are Well Adapted to Disturbances in Energy Input – Nuria Fernandez-Gonzalez – bioRxiv

Built environment microbiome

What Have We Learned about the Microbiomes of Indoor Environments? – Brent Stephens – mSystems

Bioinformatics

Cloud Computing in Bioinformatics: current solutions and challenges – Barbara Calabrese – PeerJ preprint

More microbiology

Discovery of a sesamin-metabolizing microorganism and a new enzyme – Takuto Kumano – PNAS

Microbes in the news

The Microbial Olympics 2016 – Michaeline B. Nelson – Nature Microbiology

New method improves accuracy of microbiome measurement – University of Minnesota

How To Control Eczema? With Fierce Bacterial Competition – Daniel Soo – Asian Scientist

How Miraculous Microbes Help Us Evolve Better, Faster, Stronger – Ed Yong – Smithsonian

Could this household chemical mess with your body’s microbiome? – Brian Mastroianni – CBS News

Research team uses nanoparticles to break up plaque and prevent cavities – Katherine Unger Baillie

This smells promising: Nasal bacteria pump out a new antibiotic that kills MRSA – Anna Vlasits – STAT News