Category Archives: Bik’s Non-Microbiology Picks

January 7, 2017

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3D modeling of endometrial interaction with vaginal bacteria, insect symbiont determined by host plants, 2011 tsunami effects on  phytoplankton, virus taxonomy, Microbiome Helper and microRNA sensitivity in intestinal stem cells.

Human vaginal microbiome

* Human three-dimensional endometrial epithelial cell model to study host interactions with vaginal bacteria and Neisseria gonorrhoeae – Paweł Łaniewski – Infection and Immunity

Human gut microbiome

Workshop Proceedings: Nutrition Across the Lifespan for Healthy Aging – Proceedings of a Workshop—in Brief – NAS

Review: Gut–brain axis in 2016: Brain–gut–microbiota axis — mood, metabolism and behaviour – Timothy G. Dinan & John F. Cryan – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis – Franziska Faber – PLOS Pathogens

Comparative Analysis of Drosophila melanogaster Gut Microbiota with Respect to Host Strain, Sex, and Age – Gangsik Han – Microbial Ecology

Impact of birth weight and postnatal diet on the gut microbiota of young adult guinea pigs – Kait Al – PeerJ

* Host plant species determines symbiotic bacterial community mediating suppression of plant defenses – Seung Ho Chung – Scientific Reports

Animal microbiome

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges – Gerald Lackner – PNAS

Plant, root, and soil microbiome

Regulation of root development in Arabidopsis thaliana by phytohormone-secreting epiphytic methylobacteria – Jana Klikno – Protoplasma

Diversity and composition of rhizospheric soil and root endogenous bacteria in Panax notoginseng during continuous cropping practices – Yong Tan – Journal of Basic Microbiology

Subsurface Microbial Ecosystems: A Photon Flux and a Metabolic Cascade – Alexander P. Petroff – Journal of Statistical Physics

Water microbiome

* Retrospective analysis of phytoplankton assemblages on the Iwate coast before and after the 2011 tsunami using cryopreserved DNA samples – Yutaka Okumura

Effects of iron deficiency on the growth and photosynthesis of three bloom-forming cyanobacterial species isolated from Lake Taihu – Kui Xu – Phycological Research

Patterns of bacterial diversity in the marine planktonic particulate matter continuum –
Mireia Mestre – The ISME Journal

Bioreactor, waste, and pollution microbiology

Biofilm composition and threshold concentration for growth of Legionella pneumophila on surfaces exposed to flowing warm tap water without disinfectant – Applied and Environmental Microbiology

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia – Zhiman Yang – Bioresource Technology

Accelerated acidification by inoculation with a microbial consortia in a complex open environment – Jiadong Yu – Bioresource Technology

Effects of a bacterial consortium from acid mine drainage on cadmium phytoextraction and indigenous soil microbial community – Jin-tian Li – Plant and Soil

Can DNA sequencing show differences between microbial communities in Polish and Danish wastewater treatment plants? – A. Miłobędzka – Water Science & Technology

Frequency dependent microbial growth during cycles of feast and famine – Jason Merritt – arXiv

Viruses and phages

* Consensus statement: Virus taxonomy in the age of metagenomics – Peter Simmonds – Nature Reviews Microbiology

Genomic evolution of bacterial populations under coselection by antibiotics and phage
– Johannes Cairns – Molecular Ecology

Bioinformatics and metagenomics

* Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research – André M. Comeau – mSystems

Transcriptomics

* Functional transcriptomics in diverse intestinal epithelial cell types reveals robust microRNA sensitivity in intestinal stem cells to microbial status – Bailey C.E. Peck – Journal of Biological Chemistry

Biofilms

Tackling Fungal Resistance by Biofilm Inhibitors – Shanchao Wu – Journal of Medical Chemistry

Microbes in the news

Featuring our research: The Secret Lives of Marine Mammal Microbes – Probing the mystery of what goes on inside the guts of dolphins and whales – Emma Hiolski – Scientific American

That cold you have might actually be the worst Bay Area flu outbreak in a decade – Kristin Hanes – SF Gate

Microbiomes in far-flung places: characterizing the arctic Inuit gut microbiome – Stephen Ornes – ASM

Microbes on the market

MoBio’s Microbiome News is back!

OptiBiotix Release: Microbiome Technology Powers The Healthy Weight Loss Company Expansion – BioSpace

Bik’s Non-Microbiology Picks

The crack in this Antarctic ice shelf just grew by 11 miles. A dramatic break could be imminent – Chris Mooney – Washington Post

Citizen Science: It’s that time of year: the annual bird count – Shawn Price – Los Angeles Times

November 29, 2016

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Metabolic reconstruction for 773 gut microbes, host genetics vs diet in the mouse gut, microbiology of a range of food items, and citizen scientists collecting arthropods (let’s call that microbiology today; I’m feeling generous).

Human gut microbiome
* Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota – Stefanía Magnúsdóttir – Nature Biotechnology

Animal models

* Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome – Antoine M. Snijders – Nature Microbiology

Genes, early environment sculpt the gut microbiome – EurekAlert

Animal microbiome

Compositional shifts in bacterial communities associated with the coral Palythoa caribaeorum due to anthropogenic effects – Gustavo Vasconcelos Bastos Paulino – Marine Pollution Bulletin

Plant, root, and soil microbiology

Bacterial diversity patterns differed in two developing ecosystems – Shankar G. Shanmugam – Microbial Ecology

Identifying the microbial taxa that consistently respond to soil warming across time and space – Angela M. Oliverio – Global Change Biology

Food microbiology

Exploring the microbiota of the red-brown defect in smear-ripened cheese by 454-pyrosequencing and its prevention using different cleaning systems – Raffaele Guzzon – Food Microbiology

Metagenomics reveals flavour metabolic network of cereal vinegar microbiota – Lin-Huan Wu – Food Microbiology

Monitoring of wheat lactic acid bacteria from the field until the first step of dough fermentation – Antonio Alfonzo – Food Microbiology

Exploring lot-to-lot variation in spoilage bacterial communities on commercial modified atmosphere packaged beef – Elina Säde – Food Microbiology

Characterization of the microbiota in lightly salted bighead carp (Aristichthys nobilis) fillets stored at 4 °C – Xiaochang Liu – Food Microbiology

More microbiology

An essential role for bacterial nitric oxide synthase in Staphylococcus aureus electron transfer and colonization – Traci L. Kinkel – Nature Microbiology

Staph uses nitric oxide enzyme to colonize noses – Phys.org

Microbes in the news

Gift Guide for the Grown Ups On Your List. #10. Sequence the bacteria in your gut! – Mrs Ice Cream – Hellobee

Microbiome & Nutrigenomic Medicine Seminar: Cybermonday special – gifts for you  – upcoming The Gut Institute Event in Berkeley, 10/11 December– Dr. Grace – YouTube

Microbiology in a brewery! – MicroHoldingScience

Qiagen and CosmosID launch metagenomics analysis plugin – Joe Whitworth – Food Quality News

China’s Smog Could Make It More Difficult To Fight Off Some Infections. The air pollution in Beijing has traces of antibiotic-resistant bacteria – Lindsey Pulse – Newsy.com

Bik’s Non-Microbiology Picks

The diversity of arthropods in homes across the United States as determined by environmental DNA analyses – Anne A. Madden – Molecular Ecology

Study Highlights Diversity of Arthropods Found in Homes Across the United States – From Swabs of Dust – NC State University

November 10, 2016

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Fanconi anemia, Clostridium subcluster decreased in UC, ectomycorrhizas in oak forests, cryoconite hole anaerobes.

Human oral microbiome

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia – C.P. Furquim – Journal of Dental Research

Human gut microbiome

A Single Species of Clostridium Subcluster XIVa Decreased in Ulcerative Colitis Patients – Kozue Takeshita – Inflammatory Bowel Diseases

Composition of gut microbiota in infants in China and global comparison – Ya-Shu Kuang – Scientific Reports

Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease – Paul Giacomin – Scientific Reports

Making sense of the cause of Crohn’s – a new look at an old disease – Anthony W. Segal – F1000 Research

Metaanalysis: The Emerging Role of the Gut Microbiome in Adult Patients With Multiple Sclerosis – Pamela K. Newland – Journal of Neuroscience Nursing

Review: Escherichia coli Nissle 1917 in Ulcerative Colitis Treatment: Systematic Review and Meta-analysis – Giuseppe Losurdo – Journal of Gastrointestinal and Liver Diseases

Human blood and tissue microbiology

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections – Vibeke Børsholt Rudkjøbing – BMC Infectious Diseases

Review: Mechanisms of Bacterial Colonization of Implants and Host Response – Christof Wagner – Advances in Experimental Medicine and Biology

Animal models

Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease – Ainsley M. Robinson – Inflammatory Bowel Diseases

Microbiota induces tonic CCL2 systemic levels that control pDC trafficking in steady state – M Swiecki – Mucosal Immunology

Siderophore-based immunization strategy to inhibit growth of enteric pathogens – Martina Sassone-Corsia – PNAS

Akkermansia muciniphila improves metabolic profiles by reducing inflammation in chow diet-fed mice – Shaoqian Zhao – Journal of Molecular Endocrinology

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories – François-Joël Gatesoupe – BMC Microbiology

Plant, root, and soil microbiome

Plant growth patterns in a tripartite strip relay intercrop are shaped by asymmetric aboveground competition – Chengdong Huang – Field Crops Research

First detection of Endogone ectomycorrhizas in natural oak forests – Kohei Yamamoto – Mycorrhiza

[PFD] Grape berry bacterial inhibition by different copper fungicides – Guilherme Martins – BIO Web of Conferences

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils – Z Dai – Scientific Reports

Water and extremophile microbiome

Enrichment of Cryoconite Hole Anaerobes: Implications for the Subglacial Microbiome – Marek K. Zdanowski – Microbial Ecology

Food microbiology

Sensory, microbiological and physico-chemical characterization of Klila, a traditional cheese made in the south-west of Algeria – Benamara R. N. – African Journal of MIcrobiology Research

Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced? – Bokai Zhu – Environment International

Built environment microbiology

Microbiological evaluation of drinking water available in schools in Cruz das Almas, Brazil – Marcos Vinicius Silva de Andrade – African Journal of MIcrobiology Research

Bioinformatics and metagenomics

Book chapter: DecontaMiner: A Pipeline for the Detection and Analysis of Contaminating Sequences in Human NGS Sequencing Data – Ilaria Granata – Dynamics of Mathematical Models in Biology

More microbiology

Predatory Bacteria Attenuate Klebsiella pneumoniae Burden in Rat Lungs – Kenneth Shatzkes – mBio

Predatory bacteria offer potential solution to drug resistance problem – Phys.org
Predatory Bacteria Can Cannibalize Drug-Resistant Bugs – Seeker

Bik’s non-microbiology Picks

Beyond Our Borders? Public Resistance to Global Genomic Data Sharing – Mary A. Majumder – PLOS Biology

Origins of Biodiversity – Michael J. Benton – PLOS Biology

Microbes in the news

Researchers exploring new platform for detecting pathogenic bacteria using bacteriophages – News Medical

Novel vaccines block iron scavenging by bacteria. Agents starve bacteria by raising antibodies to capture the small molecules the microbes release to harvest iron – Stu Borman – Chemical & Engineering News

What’s lurking in the water in Shedd Aquarium – Lisa Bertagnoli – Chicago Business

New biophotonic light sensor can detect Legionella bacteria in minutes – News Medical

Scrubs And Superbug Transmission In ICUs: What We Still Don’t Know Can Kill You – Judy Stone – Forbes
Dangerous bacteria could hitch a ride on nurses’ scrubs – Rachel Sereix – Duke Chronicle

Microbes and the market

Clinical Microbiology Market Expected to Reach $6.72 billion by 2022 – Medgadget

Science, publishing, and career

Rosalind’s Ghost: Biology, Collaboration, and the Female – Caroline Wagner – PLOS Biology

Differences in Collaboration Patterns across Discipline, Career Stage, and Gender – Xiao Han T. Zeng – PLOS Biology

October 21, 2016

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Oral bacteria in esophageal cancer samples, spring blooms of coastal phytoplankter, and a microbial anthropologist in the Jungle.

Events

Meeting: Chemistry of Microbiomes in Human Environments – 11/9/16 – Jonathan Eisen – MicroBEnet

Human oral microbiome

Human Microbiome Fusobacterium Nucleatum in Esophageal Cancer Tissue Is Associated with Prognosis – Kensuke Yamamura – Clinical Cancer Research

Press: Presence of certain oral bacterium in esophageal cancer samples associated with shorter survival – Medical Xpress

Human vaginal microbiome

Review: Role of microbial flora in female genital tract: A comprehensive review – Subramanyam Dasari – Asian Pacific Journal of Tropical Disease

Plant, root, and soil microbiome

Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L.) Peeling – Jiachao Zhang – PLOS ONE

Diversity indices using arbuscular mycorrhizal fungi to evaluate the soil state in banana crops in Colombia – Germán Mahecha-Vásquez – Applied Soil Ecology

Water microbiome

Physiological and ecological drivers of early spring blooms of a coastal phytoplankter – Kristen R. Hunter-Cevera – Science

Microbial community dynamics in semi-commercial RAS for production of Atlantic salmon post-smolts at different salinities – Ingrid Bakke – Aquacultural Engineering

Deep-sequencing of the bacterial microbiota in commercial-scale recirculating and semi-closed aquaculture systems for Atlantic salmon post-smolt production – Ida Rud – Aquacultural Engineering

Built environment microbiome

Shoe soles as a potential vector for pathogen transmission: a systematic review – T. Rashid – Journal of Applied Microbiology

Microbes in the news

A Microbial Anthropologist in the Jungle – Maria Gloria Dominguez-Bello – Cell

African Soil Microbiology Project – Elizabeth Bach – Global Soil Biodiversity

Researchers Say Plant Bacteria Could Provide its Own Salvation – Interesting Engineering

I’m a Doctor. If I Drop Food on the Kitchen Floor, I Still Eat It. – Aaron E. Carroll – The New York Times
Letters to the Editor: Eat Food From the Floor? Microbiology and Mores – The New York Times

Dr Brad McKay explains the complex world of vaginal bacteria – Brad McKay – News.com.au

What’s making lifeguards sick at La Jolla Cove? – Brandon Lewis – CBS8

Spotlight on Grants: Nickel and cobalt in Streptococcus – Siti Nur Amalina – Microbe Post

ASM’s Microbes After Hours Microbes After Hours: The Necrobiome – Microbial Life After Death

Bik’s Non-Microbiology Picks

We used to sell cigarettes in hospitals. 5 practices that may soon look just as outdated – Melissa Bailey – STAT News

October 13, 2016

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Ethics and microbiome research, oversimplifying microbiome studies, viruses destroy archaea in the deep seafloor, Clostridium difficile in patients sharing hospital beds.

General microbiome

Perspective: Ethical issues in microbiome research and medicine – Rosamond Rhodes – BMC Medicine

Interview: Science communication: the dangers of oversimplifying microbiome studies – Interview with Lauren Freeman and Saray Ayala – Ben Johnson – NPJ Biofilms Community

Human gut microbiome

Preview: Making It Stick: A Compelling Case for Precision Microbiome Reconstitution – David Berry – Cell Host & Microbe

Preview: A Commensal Protozoan Strikes a Balance in the Gut – P’ng Loke – Cell Host & Microbe

Animal models

Intestinal microbiota could transfer host Gut characteristics from pigs to mice – H. Diao – BMC Microbiology

Plant, root, and soil microbiome

Review: How lichens impact on terrestrial community and ecosystem properties – Johan Asplund – Biological Reviews

Water (and coral) microbiology

Virus-mediated archaeal hecatomb in the deep seafloor – Roberto Danovaro – Science Advances

Press: Deep-Sea Viruses Destroy Archaea. Viruses are responsible for the majority of archaea deaths on the deep ocean floors, scientists show – Ruth Williams – The Scientist

Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition – Sean P. McNally – Limnology and Oceanography

Food microbiology

Ultrasound improves chemical reduction of natural contaminant microbiota and Salmonella enterica subsp. enterica on strawberries – Denes Kaic Alves do Rosário – International Journal of Food Microbiology

Techniques

Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA – Daniel G. Mulcahy – PeerJ

Metagenomics

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties – C. Preston Neff – Cell Host & Microbe

Other microbiology

Division of labour in microorganisms: an evolutionary perspective – Stuart A. West – Nature Reviews Microbiology

Receipt of Antibiotics in Hospitalized Patients and Risk for Clostridium difficile Infection in Subsequent Patients Who Occupy the Same Bed – Daniel E. Freedberg – JAMA

Press: Antibiotics Encourage Spread of C.diff To Subsequent Patients Who Occupy the Same Bed and Haven’t Received Antibiotics: Interview with Daniel Freedberg – Medical Research

Microbes in the news

The Conversation Gut Series:

RI Hospital receives $500,000 CDC grant to research new approach for combating antibiotic resistance. Microbiome research will help prevent ongoing spread of multi-drug resistant bacteria – EurekAlert

Science, publishing, and career

How Are Scientists Using Social Media in the Workplace? – Kimberley Collins – PLOS ONE

5 retractions and a sack for Pfizer lead cancer researcher Min-Jean Yin – Leonid Schneider – For Better Science
Pfizer fires employee, requests five retractions – Alison McCook – Retraction Watch

Bik’s non-microbiology Picks

Genomics is failing on diversity – Alice B. Popejoy & Stephanie M. Fullerton – Nature
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations – Swapan Mallick – Nature

October 10, 2016

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A Mostly Male Microbiome meeting, host genetics and microbiota in IBD, dysbiosis in dogs and humans, airport door handles, and surfing the world for microbes. I’m back!

Events

I wish I could recommend this, but it has only 2 of the 27 invited speakers are women. This is so sad. See Jonathan Eisen’s blog post about this. Second Annual Human Microbiome Congress in San Diego / North American Microbiome Congress – 24/25 January 2017 – San Diego.

Human gut microbiome

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease – Floris Imhann – Gut

Effect of dietary interventions on the intestinal microbiota of Mongolian hosts – Jing Li – Science Bulletin

Animal models

Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks – Yoshiki Vázquez-Baeza – Nature Microbiology

Acute Infectious Gastroenteritis Potentiates a Crohn’s Disease Pathobiont to Fuel Ongoing Inflammation in the Post-Infectious Period – Cherrie L. Small – PLOS Pathogens

Press: Diarrhea-Causing Bacteria Promote Growth of Crohn’s-Linked Microbe in Mice – ET Healthworld

Neonatal androgen exposure causes persistent gut microbiota dysbiosis related to metabolic disease in adult female rats – Isabel Moreno-Indias – Endocrinology

Exposure to the Functional Bacterial Amyloid Protein Curli Enhances Alpha-Synuclein Aggregation in Aged Fischer 344 Rats and Caenorhabditis elegans – Shu G. Chen – Scientific Reports

Press: Gut microbiota may have role in neurodegenerative diseases: study – CTV News

Plant, root, and soil microbiome

Review: Too much or not enough: Reflection on two contrasting perspectives on soil biodiversity – Philippe C. Baveye – Soil Biology and Biochemistry

Built environment microbiology

Airport door handles and the global spread of antimicrobial-resistant bacteria: a cross sectional study – Frieder Schaumburg – Clinical Microbiology and Infection

Press: Are Airport Bathrooms Spreading Antibiotic-Resistant Bacteria Globally? – Alex Berezow – American Council on Science and Health

Food microbiology

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria – Kevin S. Bonham – bioRxiv

Does fingerprinting truly represent the diversity of wine yeasts? A case study with interdelta genotyping of S. cerevisiae strains – Walter P. Pfliegler – Letters in Applied Microbiology

Microbes in the news

This Surfer/PhD Student Is Scraping Bacteria off Surfers Around the World for Science – Dylan Heyden – The Inertia
Surfing the world for microbes – Erika Johnson, UC San Diego – University of California

Weethinking the role of bacteria in incontinence. Researchers look at the role of bacteria in incontinence – EurekAlert

The Unseen Cloud Makers From The Ocean – Jennifer – The Microbial Menagerie

Marine bacteria are the climate’s wild card – ScienceNordic

Researchers Hunt for a Link Between Microbiome and Autism – KQED

The natural wonder that holds the key to the origins of life – and warns of its destruction – Michael Slezak – The Guardian

Did his artificial hips put him at risk of infection when he saw the dentist? – David Lindley – Washington Post

Millions of craft paint units recalled over bacteria concerns – Morgan Maria Pawl – KDVR

Science, publishing, and career

Scientific Misconduct: The Elephant in the Lab. A Response to Parker et al. – Timothy D. Clark – Trends in Ecology & Evolution

Bik’s non-microbiology Picks

As DNA reveals its secrets, scientists are assembling a new picture of humanity – Carl Zimmer

September 12, 2016

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Individual response of gut microbiota to diet (in mice), appendicitis, adaptive evolution of goose with its microbiome, fungi in rubber plantations.

Events

Storify of days 1-2 of the 6th ASM Beneficial Microbes Meeting, Sept 9-12, Seattle, WA.

Pregnancy and birth

Urinary Microbiota Associated with Preterm Birth: Results from the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) Study – Nicholas J. Ollberding – PLOS ONE

Review: The role of the bacterial microbiota on reproductive and pregnancy health – Deborah B. Nelson – Anaerobe

Human skin microbiome

Skin microbiome prior to development of atopic dermatitis: early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year – Elizabeth A. Kennedy – Journal of Allergy and Clinical Immunology

Human respiratory microbiome (and Methods)

Note that 2 different amplification strategies were performed, so IMHO this is more reflection of primer differences than sequencing differences: Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum – Andrea Hahn – Journal of Microbiological Methods

Human gut microbiome

Evaluation of the microbiome in children’s appendicitis – Martin Salö – International Journal of Colorectal Disease

Review: Food: a new form of personalised (gut microbiome) medicine for chronic diseases? – Tess Pallister – Journal of the Royal Society of Medicine

Review: Linking the Microbiota, Chronic Disease, and the Immune System – Timothy W. Hand – Trends in Endocrinology & Metabolism

Animal and bioreactor experiments

From the Sonnenburg lab @Stanford: Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice – Samuel A. Smits – mSystems

An In Vitro Approach to Study Effects of Prebiotics and Probiotics on the Faecal Microbiota and Selected Immune Parameters Relevant to the Elderly – Yue Liu – PLOS ONE

Animal microbiome

Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose – Guangliang Gao – Scientific Reports

Hold off on the orange oil: Characterization of Antibacterial Activities of Eastern Subterranean Termite, Reticulitermes flavipes, against Human Pathogens – Yuan Zeng – PLOS ONE

Use of MALDI-TOF MS and culturomics to identify mosquitoes and their midgut microbiota – Fatalmoudou Tandina – Parasites & Vectors

Plant, root, and soil microbiome

Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event – Lucia Fuchslueger – Journal of Ecology

Effect of organic matter enrichment on the fungal community in limestone cave sediments – ELS Marques – Genetics and Molecular Research

Contrasting elevational diversity patterns for soil bacteria between
two ecosystems divided by the treeline – Guixiang Li – Science China Life Sciences

Review: Diversity and ecology of soil fungal communities in rubber plantations – Jutamart Monkai – Fungal Biology Reviews

Illumina sequencing reveals a rhizosphere bacterial community associated with foxtail millet smut disease suppression – Yansha Han – Plant and Soil

Water and extremophile microbiome

Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments – Mustafa Adel – Scientific Reports

Built environment microbiome

Review: The Microbiome of the Built Environment and Human Behavior: Implications for Emotional Health and Well-Being in Postmodern Western Societies – C.E. Stamper – International Review of Neurobiology

Microbes in the news

The Bacteria on Your Skin Are Safer Than These Two Chemicals the FDA Just Banned From Your Soap – Jill Richardson – Truth Digg

DNA in London Grave May Help Solve Mysteries of the Great Plague – Roff Smith – National Geographic

Bik’s Non-Microbiology Picks

This paper was discussed on Twitter this weekend because of a conflict of interest of one of the authors (Deepak Chopra) and the design and interpretation of the study:

Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI) – Christine Tara Peterson – Scientific Reports

September 10, 2016

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Bifidobacteria and ulcerative colitis, the pollen microbiome, busting the 5-second rule, resistance genes in 23,000 microbial genomes, and a cool video of evolution of bacterial resistance.

Events

Gut health, microbiota & probiotics throughout the lifespan – Metabolic & Brain function 2016 – Sept 15-16, Harvard Medical School, Boston, MA

Human oral microbiome

Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma – Haifeng Lu – Scientific Reports

Human respiratory microbiome

Review: The microbiome in asthma – Magali Noval Rivas – Current Opinion Pediatrics

Human gut microbiome

Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers – Sabrina Duranti – FEMS Microbiology Ecology

Review: Gut Microbiota, Inflammation, and Colorectal Cancer – Caitlin A. Brennan – Annual Review of Microbiology

Review: Microbiota—myeloid cell crosstalk beyond the gut – Sayeh Gorjifard – Journal of Leukocyte Biology

Four reviews in Current Pharmaceutical Design in the category “Could the gut microbiota perhaps be involved in disease X?” – with 4 different X’s. 

Animal models

Antibiotic Treatment Induces Long-lasting Changes in the Fecal Microbiota that Protect Against Colitis – Naomi L. Ward – Inflammatory Bowel Diseases

Differences In CD8αα And Cecal Microbiome Community During Proliferation And Late Cytolytic Phases Of Marek’s Disease Virus (MDV) Infection Are Associated With Genetic Resistance To Marek’s Disease – Sudeep Perumbakkam – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity – Binoy Ambika Manirajan – Environmental Microbiology

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria – Teotonio Soares de Carvalho – Ecology

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil – Martina Štursová – FEMS Microbiology Ecology

Extremophile microbiome

Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns – Leonardo Di Meglio – FEMS Microbiology Ecology

Built environment microbiome

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Christin Lola / Fotolia (via Science Direct)

Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food – Robyn C. Miranda – Applied and Environmental Microbiology

Researchers debunk ‘five-second rule’: Eating food off the floor isn’t safe. Sometimes bacteria transfer in less than a second – Science Daily

Forget the ‘five-second rule’: Food dropped on the floor picks up bacteria in just ONE second – David Gardner – Daily Mail

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome – Erica M. Hartmann – Environmental Science & Technology

Antibiotic Resistance Genes in Indoor Dust – Technology Networks

Metagenomics and bioinformatics

The transfer network of bacterial mobile resistome connecting animal and human microbiome – Yongfei Hu – Applied and Environmental Microbiology

Catalog of Mobile Antibiotic Resistance Genes Helps Explain Transfer to Human Pathogens – Genome Web

Chinese investigators characterize the world of resistance gene exchange among bacteria – Phys.org

Phages and viruses

Bacteriophages in clinical samples can interfere with microbiological diagnostic tools – Maryury Brown-Jaque – Scientific Reports

Techniques

Absolute quantification of microbial taxon abundances – Ruben Props – The ISME Journal

Microbes in the news

Jo Handelsman of White House Office of Science and Technology to Speak Monday – University of Tennessee

WATCH: Bacteria Invade Antibiotics And Transform Into Superbugs – Angus Chen – NPR
This might be the coolest visualization of evolution ever. Watch these bacteria evolve antibiotic resistance in just 12 days – Brian Resnick – Vox

These researchers would like you to mail them your gut bacteria – Katherine Lindemann – Research Gate Blog

Hepatitis A Outbreak Linked to Strawberries at Smoothie Chain – Daniel Victor – New York Times

Bacteria Hysteria

M&S becomes first supermarket to offer anti-bacterial shopping bags to banish bugs such as E. coli –  Katie Morley – The Telegraph

Bik’s non-microbiology Picks

Microbiome analysis, please! Giraffes aren’t just giraffes. Turns out there are four species – Rachel Feltman – Washington Post

Flatworm parasite named after Barack Obama: Is that a compliment? – Rowena Lindsay Christian Science Monitor

 

August 31, 2016

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Screen Shot 2016-08-31 at 10.36.09 PM

ICU, Rudlavibizon, Flickr

Gut microbiota changes in the ICU, air microbiome of the Gobi desert, host response of human cells to gut microbiota.

Event

Synbiobeta SF2016, October 4-6, South San Francisco, CA

Human gut microbiome

Extreme Dysbiosis of the Microbiome in Critical Illness – Daniel McDonald – mSphere

Press: ICU patients lose helpful gut bacteria within days of hospital admission – Science Daily
Tracking Bacterial Imbalance in the ICU – Stephen Ornes -mBiosphere

Review: The human gut microbiome, diet, and health: “post hoc non ergo propter hoc” – Guus Roeselers – Trends in Food Science & Technology

Review: Interplay between gut microbiota, its metabolites and human metabolism: dissecting cause from consequence – A.V. Hartstra – Trends in Food Science & Technology

Animal and other model experiments

Bidirectional communication between the Aryl hydrocarbon Receptor (AhR) and the microbiome tunes host metabolism – Agata Korecka – NPJ Biofilms and Microbiomes

Temporal dynamics of bacterial microbiota in the human oral cavity determined using an in situ model of dental biofilms – Nanako Wake – NPJ Biofilms and Microbiomes

Normalizing Microbiota-Induced Retinoic Acid Deficiency Stimulates Protective CD8+ T Cell-Mediated Immunity in Colorectal Cancer – Nupur Bhattacharya – Immunity

Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota – Allison L. Richards – mSystems

Animal microbiome

Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement – Darren J Parris – PeerJ

Plant, root, and soil microbiome

Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity – Zhilin Yuan – Scientific Reports

A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities – Renee B. Johansen – Fungal Ecology

Bacterial community structure and function shift across a northern boreal forest fire chronosequence – Hui Sun – Scientific Reports

Water microbiome

Complex bacterial communities in the deep-sea sediments of the Bay of Bengal and volcanic Barren Island in the Andaman Sea – Pankaj Verma – Marine Genomics

Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension – Craig J. Plante – Journal of Phycology

Air microbiome

Variations in the structure of airborne bacterial communities in Tsogt-Ovoo of Gobi desert area during dust events – Teruya Maki – Air Quality, Atmosphere & Health

Bioinformatics and metagenomics

A phylogenetic transform enhances analysis of compositional microbiota data – Justin D Silverman – bioRxiv

Higher classification sensitivity of short metagenomic reads with CLARK-S – Rachid Ounit – Bioinformatics

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly – Cuncong Zhong – BMC Bioinformatics

Microbial ecology

Quantifying human impact on Earth’s microbiome – Stephen B. Pointing – Nature Microbiology

Synthetic microbial ecology and the dynamic interplay between microbial genotypes –
Jan Dolinšek – FEMS Microbiology Reviews

Microbes in the news

Engineered gut bacteria protect mice against obesity, improve liver function – Oliver Worsley – Fierce Biotech

You’re probably not doing metagenomics – Mick Watson – Opiniomics

Mayo Adds To Its List Of Gut Microbiome Startup Collaborators – Don Jacobson – Twin Cities Business

Nice analysis of Tweets from #ISME16 by Keith Turner – Jonathan Eisen – MicroBEnet

Peer review and science misconduct

Recognizing Peer Reviewers: a Webinar to Celebrate Editors and Researchers – September 19, 2016 – Elsevier Publishing Campus

Stop ignoring misconduct – Donald S. Kornfeld & Sandra L. Titus – Nature

Bik’s Non-Microbiology Picks

Paperfuge: An ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy – M. Saad Bhamla – bioRxiv

August 30, 2016

Posted on by
Screen Shot 2016-08-30 at 11.07.12 PM

Red-shanked douc, Wikipedia

The human gut phageome, monkey microbiome humanizes in captivity, and a Yersinia genome from the 6th century (OK, that’s not microbiome, but just cool).

Human gut microbiome

Healthy human gut phageome – Pilar Manrique – PNAS

Press: Your Gut’s Gone Viral, And That Might Be Good For Your Health – Michaeleen Doucleff – NPR

Animal experiments

Standardizing Mouse Models to Account for Host–Microbial Interactions – Maria-Luisa Alegre – American Journal of Transplantation

Note: no mention of blanks/extraction controls: Consumption of a high-fat diet alters the seminal fluid and gut microbiomes in male mice – Angela B. Javurek – Reproduction , Fertility and Development

Animal microbiome

Captivity humanizes the primate microbiome – Jonathan B. Clayton – PNAS

Press (also see yesterday’s post): Gut biome of monkeys found to change when they are kept in captivity – Bob Yirka – Phys.org
Monkeys in zoos have human gut bacteria – Science Daily

Water microbiome

Coastal connectivity and spatial subsidy from a microbial perspective – Christin Säwström – Ecology and Evolution

Taxonomic profiling of bacterial community structure from coastal sediment of Alang–Sosiya shipbreaking yard near Bhavnagar, India – Vilas Patel – Marine Pollution Bulletin

Proteobacteria become predominant during regrowth after water disinfection – Cristina Becerra-Castro – Science of the Total Environment

Microbial Ecology

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology – Ed Hall – bioRxiv

More microbes

A high-coverage Yersinia pestis Genome from a 6th-century Justinianic Plague Victim – Michal Feldman – Molecular Biology and Evolution

Press: World’s 1st Plague Pandemic Bacteria Gets New Genetic Analysis – Greg Uyeno – Live Science
Why scientists reconstructed an ancient plague – Nikki Ferlaino – KFOR
Reconstructing the sixth century plague from a victim – Phys.org
The Same Microbe That Led to Black Death Also Caused a Huge Plague Centuries Before – Jennifer Ouellette – Gizmodo
Medieval victim reveals secrets of the Plague of Justinian – Gretchen Vogel – Science

Microbes in the news

Hand dryers spread bacteria, affect health on campus – Shane Olney – The Volante

Science, publishing, and career

A Framework for Improving the Quality of Research in the Biological Sciences – Arturo Casadevall – mBio

Bik’s Non-Microbiology Picks

Dental calculus reveals Mesolithic foragers in the Balkans consumed domesticated plant foods – Emanuela Cristiani – PNAS

Surprisingly Little Evidence for the Accepted Wisdom About Teeth – Aaron E. Carroll – New York Times