Category Archives: Human oral

June 15, 2016

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Microbiome evolution in vertebrates, post-antibiotic microbial competition for sugars, microbial networks in respiratory infections, bacteria in snow from Australian and Swiss Alps, Yucatan Black and Red soil microbes.

Human oral microbiome

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients – Michael J Cox – bioRxiv

Human skin microbiome

Comprehensive pyrosequencing analysis of the bacterial microbiota of the skin of patients with seborrheic dermatitis – Akiomi Tanaka – Microbiology and Immunology

Review: Can molecular DNA-based techniques unravel the truth about diabetic foot infections? – M. Malone – Diabetes/Metabolism Research and Reviews

Human respiratory microbiome

Mycoplasma pneumoniae and Streptococcus pneumoniae caused different microbial structure and correlation network in lung microbiota – Heping Wang – Journal of Thoracic Disease

Human gut microbiome

Ecophysiological consequences of alcoholism on human gut microbiota: implications for ethanol-related pathogenesis of colon cancer – Atsuki Tsuruya – Scientific Reports

Research highlight: Intimate gut interactions: helminths and the microbiota – Nicola L Harris – Cell Research

Review: Human Gut-on-a-Chip technology: Will this revolutionize our understanding of IBD and future treatments? – Jaewon Lee – Expert Review of Gastroenterology & Hepatology

Review: Dientamoeba fragilis, the Neglected Trichomonad of the Human Bowel – Damien Stark – Clinical Microbiology Reviews

Review: Akkermansia muciniphila: a novel functional microbe with probiotic properties – C. Gómez-Gallego – Beneficial Microbes

Review: Alterations of gut microbiota in patients with irritable bowel syndrome: A systematic review and meta-analysis – Xiaojun Zhuang – Journal of Gastroenterology and Hepatology

Animal and tissue culture experiments

Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion – Franziska Faber – Nature

News and Views: Microbiology: The dark side of antibiotics – Thibault G. Sana & Denise M. Monack – Nature

Genetic and transcriptional analysis of human host response to healthy gut microbiome – Allison L Richards – bioRxiv

The Microbiota Determines Susceptibility to Experimental Autoimmune Uveoretinitis – Jarmila Heissigerova – Journal of Immunology Research

Animal microbiome

Invited Review: Microbiome Evolution Along Divergent Branches of the Vertebrate Tree of Life: What’s Known and Unknown – Timothy J. Colston – Molecular Ecology

Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity – Swapnil Gaikwad – AMB Express

Plant, root, and soil microbiome

Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.) – Wenfeng Wang – Microbiological Research

Yucatán in black and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community structures in the two main kinds of soil of Yucatán State – Héctor Estrada-Medina – Microbiological Research

Water and extremophile microbiome

Global and local-scale variation in bacterial community structure of snow from the Swiss and Australian Alps – Tina Wunderlin – FEMS Microbiology Ecology

Waste, pollution, drinking water microbiology

Assessing the effects of heavy metals in ACC deaminase and IAA production on plant growth-promoting bacteria – Mendoza-Hernández José Carlos – Microbiological Research

Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants – Devin B. Holman – PLOS ONE

Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities – Lucélia Cabral – Environmental Pollution

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms – Zsuzsanna Nagymáté – Microbiological Research

A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time – Peter A. Noble – Applied Microbiology and Biotechnology

DGGE: Synergistic effect of crude oil plus dispersant on bacterial community in a louisiana salt marsh sediment – Mohammed Al-Jawasim – FEMS Microbiology Letters

Food microbiology

Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space – Marinella Marzano – PLOS ONE

More microbiology

Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B – Caroline Chénard – mBio

Press: Virus Hacks Host Genome, Steals CRISPR to Protect Itself – GenEngNews
Virus uses ‘stolen’ CRISPR to hack its host’s immune system – Science Daily

Microbes in the news

Asgard archaea diversity in estuaries – Roy Rodriguez – REU in Subtropical Marine Ecosystems, University of Texas at Austin

Microbes in pressed grapes may predict flavor metabolites in the finished wine – American Society for Microbiology – EurekAlert

Nanoflowers can detect bacteria before they make you sick: The particles can spot even tiny amounts of E. coli – Mariella Moon – Engadget

BacteriaHysteria: Self-cleaning sheets do exist! Silvon launches bacteria-resistant bedding – Julie Pennell – Today

Science, publishing, and career

Predatory journals: Ban predators from the scientific record – Jeffrey Beall – Nature

Data sharing: A code of conduct for data on epidemics – Ilaria Capua – Nature

June 10, 2016

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Volunteers taking ETEC, 3 new E. coli phages, oral microbiomes of cats and dogs, skin microbes in Japanese amphibians, fungi and bacteria in floor dust.

Human oral microbiome

The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals – Jordan E. Bisanz – PeerJ

Human vaginal microbiome

Association of Sexual Debut in Adolescents With Microbiota and Inflammatory Markers – Jespers, Vicky – Obstetrics & Gynecology

Human blood ‘microbiome’

Rapid identification of fungi in culture-negative clinical blood and respiratory samples by DNA sequence analyses – Farida Sidiq – BMC Research Notes

Human gut microbiome

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment – Mihai Pop – BMC Genomics

Mucosa-Associated Ileal Microbiota in New-Onset Pediatric Crohn’s Disease – Assa, Amit – Inflammatory Bowel Diseases

Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy – Marion Dalmasso – PLOS ONE

“Free living females” sounded… weird. Soluble Corn Fiber Increases Calcium Absorption Associated with Shifts in the Gut Microbiome: A Randomized Dose-Response Trial in Free-Living Pubertal Females – Corrie M Whisner – Journal of Nutrition

Similar Fecal Microbiota Signatures in Patients With Diarrhea-predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

DGGE: Differences in the Biodiversity of the Fecal Microbiota of Infants With Rotaviral Diarrhea and Healthy Infants – Peng Fei – Jundishapur Journal of Microbiology

Opinion: How Our Other Genome Controls Our Epi-Genome – Antonella Celluzzi – Trends in Microbiology

Review: The role of the gut microbiota in NAFLD – Christopher Leung – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Diet may influence the oral microbiome composition in cats – Christina J. Adler – Microbiome

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules – James E. McDonald – PLOS ONE

Bacterial microbiomes from vertically-transmitted fungal inocula of the leaf-cutting ant Atta texana – Lucas A. Meirelles – Environmental Microbiology Reports

Defensive insect symbiont leads to cascading extinctions and community collapse – Dirk Sanders – Ecology Letters

Plant, root, and soil microbiome

Subalpine conifers in two different geographic locations host highly similar foliar bacterial endophyte communities – Alyssa A. Carrell – FEMS Microbiology Ecology

Effect of plant growth-promoting bacteria on the growth and fructan production of Agave americana L. – Neyser De La Torre-Ruiz – Brazilian Journal of Microbiology

Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region – Joana Sabino-Pinto – Microbial Ecology

Water and extremophile microbiome

Benthic protists: the under-charted majority – Dominik Forster – FEMS Microbiology Ecology

Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance – Maren Bornemann – FEMS Microbiology Ecology

Review: How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes – Elena Kazamia – Ecology Letters

Review: All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Pollution and waste and bioreactor microbiology

Arsenic metabolism and toxicity influenced by ferric iron in simulated gastrointestinal tract and the roles of gut microbiota – Haiyan Yu – Environmental Science & Technology

Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation – Saranya Kuppusamy – Journal of Hazardous Materials

A strange combination of samples: Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies – Simon Güllert – Biotechnology for Biofuels

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing – S. Festa – FEMS Microbiology Ecology

Built environment microbiome

Fungal and bacterial growth in floor dust at elevated relative humidity levels – Karen C. Dannemiller – Indoor Air

Bioinformatics and statistics

An Introduction to Programming for Bioscientists: A Python-Based Primer – Berk Ekmekci – PLOS Computational Biology

Ten Simple Rules for Effective Statistical Practice – Robert E. Kass – PLOS Computational Biology

Bipartite Graphs for Visualization Analysis of Microbiome Data – Karel Sedlar – Evolutionary Bioinformatics

Techniques

The source of SYBR green master mix determines outcome of nucleic acid amplification reactions – Jianxin Yang – BMC Research Notes

More microbiology

Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes – Florian Busch – Cell Chemical Biology

Press: Ancient enzyme resurrected from the ancestor of all bacteria – Conor Gearin – New Scientist
Bacteria perfected protein complexes more than 3.5 billion years ago – Science Daily

Microbes in the news

Tufts microbiologist Cecilia A. Silva-Valenzuela, Ph.D., named Pew Latin American Fellow
Silva-Valenzuela, in Andrew Camilli’s lab, will investigate novel approaches to prevent cholera outbreaks – EurekAlert

Bio-statistician Albert Parker with MSU’s Center for Biofilm Engineering earns top EPA award – Amanda Eggert – Montana State University

Video series with James Hamblin – The Atlantic
Should You Map Your Microbiome? A visit to uBiome
Your Probiotics Aren’t Doing Anything (Yet)
You Probably Don’t Need to Shower – James Hamblin – The Atlantic

Banking on stool despite an uncertain future – Tina Amirtha – Science

Science, publishing, and career

In effort to understand continuing racial disparities, NIH to test for bias in study sections – Jeffrey Mervis – Science

Triplicated paper with multiplicated cells and images – Leonid Schneider – For Better Science
Author denies accusations of blatant duplication – Shannon Palus – Retraction Watch

Bik’s Picks (it’s not microbiology, but pretty cool)

RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation – Christian Jeudy – Plant Methods

June 9, 2016

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Salivary microbiome in Behcet’s disease, microbial RNA in human blood, acetate implied in metabolic syndrome, effects of fire retardant on plant–microbe interactions, and a book about the marine microbiome.

Events

ASM Microbe TweetUp: Friday June 17, 11.45-12:30, in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Focused meeting: Molecular Biology of Archaea 5, London, UK, 1-3 August 2016

Pregnancy and birth

Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus – Valeria Sagheddu – Frontiers in Pediatrics

Review: The microbiome during pregnancy and early postnatal life – Josef Neu – Seminars in Fetal and Neonatal Medicine

Review: The human milk microbiome and factors influencing its composition and activity – Carlos Gomez-Gallego – Seminars in Fetal and Neonatal Medicine

Human blood microbiome

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects – Serghei Mangul – bioRxiv

Human mouth microbiome

A Study of the Variation in the Salivary Peptide Profiles of Young Healthy Adults Acquired Using MALDI-TOF MS – Andrei Prodan – PLOS ONE

Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet’s disease – Patrick Coit – Clinical Immunology

Human gut microbiome

Review: What’s bugging your teen? —The microbiota and adolescent mental health – Karen-Anne McVey Neufeld – Neuroscience & Biobehavioral Reviews

Bio-banking gut microbiome samples – Shankar Bolan – EMBO Reports

Animal experiments

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome – Rachel J. Perry – Nature

Press: How altered gut microbes cause obesity – Science Daily
Fecal Transplant Shows Gut Microbes Cause Obesity – In Rats, Anyway – Science 2.0

Sex-specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome – Liang Chi – Chemical Research in Toxicology

Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches – Fuyong Li – Frontiers in Microbiology

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan – Environmental Microbiology

Animal microbiome

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Cascading effects of fire retardant on plant–microbe interactions, community composition, and invasion – Abigail Marshall – Ecological Applications

Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Journal of Geophysical Research

Selection and evaluation of microorganisms for biocontrol of Verticillium dahliae in olive – A Varo – Journal of Applied Microbiology

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils – Anna Poli – Fungal Biology

Arbuscular mycorrhizal fungal communities in buffelgrass pasture under intercropping and shading systems in Brazilian semiarid conditions – Karen M.S. Menezes – Agriculture, Ecosystems & Environment

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression – Adam J. Book – PLOS Biology

Press: Chemistry lessons from bacteria may improve biofuel production – Science Daily

Review: Streptomyces as a plant’s best friend? – Tom Viaene – FEMS Microbiology Ecology

Water and extremophile microbiome

Light availability regulates the response of algae and heterotrophic bacteria to elevated nutrient levels and warming in a northern boreal peatland – Lily Y. Gu – Freshwater Biology

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Microbial community structure of Arctic seawater as revealed by pyrosequencing – Yang Li – Acta Oceanologica Sinica

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean – Jing Wang – Acta Oceanologica Sinica

Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina – Laura T. Carney – Algal Research

Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation – Zothanpuia – PeerJ

Microbial diversity in lake–river ecotone of Poyang Lake, China – Xiaolan Huang – Environmental Earth Sciences

Book: The Marine Microbiome. An Untapped Source of Biodiversity and Biotechnological Potential – Lucal J. Stal, Mariana Silvia Cretoiu – Springer

Food microbiology

Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese – Davide Porcellato – International Dairy Journal

Pollution and waste microbiology

Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters – Daniel Carey – Environ Sci Processes Impacts

Computational models of microbiome research, bioinformatics

Synergistic elimination of bacteria by phage and the immune system – Chung Yin (Joey) Leung – bioRxiv

A new way to publish metagenomics studies – Folker Meyer – BioMed Central

Techniques

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes – Tillmann Lueders – Current Opinion in Biotechnology

More microbiology

Centenary of the death of Elie Metchnikoff: A visionary and an outstanding team leader –
Jean-Marc Cavaillon – Microbes and Infection

Microbes in the news

Worcester Polytechnic Institute Students Isolate Potentially Novel Soil-Dwelling Viruses – PR Web

Yuck factor may boost hand hygiene compliance: Interview with Ashley Gregory – EurekAlert

Europe orders Italians to cut down olive trees infected with bacteria – Nick Squires – The Telegraph

It’s Not Just Restaurants—Scientists Are Fascinated With Fermented Foods Too – Jane Lear – Take Part

Science, publishing, and career

Differences in incomes of physicians in the United States by race and sex: observational study – Dan P. Ly – British Medical Journal

Press: White male doctors earn 35 percent more than black male doctors – Jennifer Adaeze Okwerekwu – STAT News

June 6, 2016

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Human oral microbiome

Identification of oral bacteria on titanium implant surfaces by 16S rDNA sequencing – Fabiana de Melo – Clinical Oral Implants Research

Subgingival microbiota in individuals with severe chronic periodontitis – Chi-Ying Tsai – Journal of Microbiology, Immunology and Infection

Human gut microbiome

Gut to brain interaction in Autism Spectrum Disorders: a randomized controlled trial on the role of probiotics on clinical, biochemical and neurophysiological parameters – Elisa Santocchi – BMC Psychiatry

Review: Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health – Helen Wasielewski – Annals of the New York Academy of Sciences

Press: War and peace in the human gut: probing the microbiome -Biodesign

Animal and tissue culture experiments

Adult microbiota-deficient mice have distinct dendritic morphological changes: differential effects in the amygdala and hippocampus – Pauline Luczynski – European Journal of Neuroscience

Exposure to common respiratory bacteria alters the airway epithelial response to subsequent viral infection – Carla Bellinghausen – Respiratory Research

Animal microbiome

Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae) – Maxi Snyman – World Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages – Shengjing Shi – Ecology Letters

Functional Role of Bacteria from Invasive Phragmites australis in Promotion of Host Growth – M. A. Soares – Microbial Ecology

Design defines the effects of nanoceria at a low dose on soil microbiota and the potentiation of impacts by canola plant – Mohamed Hamidat – Environmental Science & Technology

Water and extremophile microbiome

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap – Jarishma K. Gokul – Molecular Ecology

Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic – Sunil Mundra – MicrobiologyOpen

Microbial sedimentary imprint on the deep Dead Sea sediment – Camille Thomas – The Depositional Record

Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand – Nick H. Secker – Journal of Phycology

Abundance of sulfur-degrading bacteria in a benthic bacterial community of shallow sea sediment in the off-Terengganu coast of the South China Sea – Zahar Marziah – MicrobiologyOpen

Pollution and waste microbiology

Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing – Lei Wang – Marine Pollution Bulletin

Effects of erythromycin, trimethoprim and clindamycin on attached microbial communities from an effluent dominated prairie stream – M.J. Waiser – Ecotoxicology and Environmental Safety

Metagenomics and bioinformatics

MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data – Vladimir I. Ulyantsev – Bioinformatics

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses – Vanni Bucci – Genome Biology

Microbes in the news

New Bacterial Research May Help Reduce Excessive Amounts Of Phosphorus In Lakes –
Catherine Cabral-Isabedra – Tech Times

About Nicholas Muzyczka, microbiology professor at the University of Florida: Inventor says fame is fine, but best reward is helping others – Anthony Clark – Gainesville.com

Bacteria has potential to clean up oil spills – Zia Lyle – Daily Texan Online

Clif Bars join list of products recalled over listeria concern – Debra Goldschmidt – CNN

Microbes in Space: JPL Researcher Explores Tiny Life – NASA

Jason Tetro aims to rehabilitate microbes’ bad reputation with The Germ Files – Rebecca Tucker – National Post

Science, publishing, and career

Publishing for academic refugees: Paul Ostwald: The Journal of Interrupted Studies – Emma Christie – Oxford Student

Postdoc mysteries: three recent developments raise puzzling uncertainties about postdocs’ present and future lives – Beryl Lieff Benderly – Science

June 2, 2016

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Neck radiation and oral pathogen increase, menopause and the vaginal microbiome, nectar microbes, raw camel milk, and a review on short-chain fatty acids.

Human skin microbiome

Review: Microbial Ecology of the Human Skin – Anthony M. Cundell – Microbial Ecology

Human oral microbiome

Head and neck intensity modulated radiation therapy leads to an increase of opportunistic oral pathogens – Jennifer M. Schuurhuis – Oral Oncology

Human respiratory microbiome

Airway Microbiota Determines Innate Cell Inflammatory or Tissue Remodeling Profiles in Lung Transplantation – Eric Bernasconi – American Journal of Respiratory and Critical Care Medicine

Human vaginal microbiome

Review: Menopause and the Vaginal Microbiome – Alicia L. Muhleisen – Maturitas

Human gut microbiome

Not sure why this got published in Neurocomputing, also very poor English:
Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing – Jian-Lei Gu – Neurocomputing

Commentary: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Complex Relationships Between Food, Diet, and the Microbiome – Laura A. Pace – Gastroenterology Clinics of North America

Animal microbiome

Caribbean corals house shared and host-specific microbial symbionts over time and space – Nathaniel D. Chu – Environmental Microbiology Reports

Genome evolution and nitrogen-fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches – Vera Tai – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators – Rachel L. Vannette – Ecology

The Root-Associated Microbial Community of the World’s Highest Growing Vascular Plants – Roey Angel – Microbial Ecology

Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities – Xia Yuan – Ecology

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest – Erik M. Schilling – Oecologia

Metal contamination status of the soil-plant system and effects on the soil microbial community near a rare metal recycling smelter – Zhu Li – Environmental Science and Pollution Research

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests – Stephanie N. Kivlin – Environmental Microbiology

Review: Emerging Insights on Brazilian Pepper Tree (Schinus terebinthifolius) Invasion: The Potential Role of Soil Microorganisms – Karim Dawkins – Frontiers in Plant Science

Food microbiology

Bacteriological quality of raw camel milk along the market value chain in Fafen zone, Ethiopian Somali regional state – Tsegalem Abera – BMC Research Notes

Bioreactor microbiology

Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors – Sung Jun Jo – Water Research

Phages and viruses

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction – Hadrien Delattre – Virology

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes – Branko Rihtman – PeerJ

Metagenomics and bioinformatics

Identification and analysis of integrons and cassette arrays in bacterial genomes – Jean Cury – Nucleic Acids Research

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing – Claudio Donati – Nature Microbiology

Improved metagenome screening efficiency by random insertion of T7 promoters – Yu Jung Kim – Journal of Biotechnology

Experiences in integrated data and research object publishing using GigaDB – Scott C Edmunds – International Journal on Digital Libraries

Techniques

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples – Satyabrata Bag – Scientific Reports

Proteomics, metabolomics

In vitro metabolic labeling of intestinal microbiota for quantitative metaproteomics – Xu Zhang – Analytical Chemistry

Syntrophic metabolism of vitamins and amino acids in gut microbial community as revealed by in silico genomic analyses – Matvei Sergeevich Khoroshkin – The FASEB Journal

Review: From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites – Ara Koh – Cell

More microbiology

Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories – N. Wurtz – European Journal of Clinical Microbiology & Infectious Diseases

Effects of temperature variability on community structure in a natural microbial food web – Axel Zander – Global Change Biology

Perspective: Cooperative Microbial Tolerance Behaviors in Host-Microbiota Mutualism – Janelle S. Ayres – Cell

Review: Multifaceted Interfaces of Bacterial Competition – Reed M. Stubbendieck – Journal of Bacteriology

Microbes in the news

Featuring our former lab member Kate Rubins: Napa native heading to International Space Station on 1st space mission – ABC7news

American Gut Project Expands to Asia – Crowdsourced microbiome sequencing effort seeks participant diversity – Heather Buschman – UC San Diego Health

Making sense of microbiomes – UCI biochemist studies the effect of unique virus, bacteria and fungi on kids’ health – Tom Vasich – UCI News

11 deaths at Huntington Hospital among patients infected by dirty scopes, city report says – LA Times
Deadly dirty medical scopes still threaten trusting patients – My News LA

Walnuts may improve your colon health: Eating walnuts changes the gut microbiome and reduces cancer growth – EurekAlert

Gluten-Free Diet Induces Changes In Gut Microbiome – Interview with Ettje Tigchelaar – Medical Research

Fecal Transplants Effective for Healing Ulcerative Colitis – HCP Live

Gut Microbiome Tied to Metabolic Hormones in Early Pregnancy – Doctors Lounge

Human Gut Microbiome May Help Identify New Ways of Preventing and Treating Diabetes – Endocrinology Advisor

Researchers poo poo antibiotics – Vet Practice Magazine

Video: Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community – Vizbi

Cold shock: E.coli bacteria found in 92 per cent ice samples in Mumbai – MidDay

Science, publishing, and career

The scientist’s guide to summer reading – Science

What does scientific reproducibility mean, anyway? – Ivan Oransky and Adam Marcus – STAT News

May 30, 2016

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Blogging from AMS Airport, with just a couple of new papers that came out yesterday.

Pregnancy and birth

Randomized Control Trial of Human Recombinant Lactoferrin: A Substudy Reveals Effects on the Fecal Microbiome of Very Low Birth Weight Infants – Michael P. Sherman – The Journal of Pediatrics

Editorial: Clinical Benefits of Lactoferrin for Infants and Children – Paolo Manzoni – The Journal of Pediatrics

Human oral microbiome

Initial oral biofilm formation on titanium implants with different surface treatments: An in vivo study – Cyntia Ferreira Ribeiro – Archives of Oral Biology

Human gut microbiome

Research Highlight: Helminths and Intestinal Flora Team Up to Improve Gut Health – Paul Giacomin – Trends in Parasitology

Plant, root, and soil microbiome

How to live with phosphorus scarcity in soil and sediment: Lessons from bacteria.– Yunuen Tapia-Torres – Applied and Environmental Microbiology

Waste and pollution microbiology

Evolution of microbial community along with increasing solid concentration during high-solids anaerobic digestion of sewage sludge – Can Liu – Bioresource Technology

Is there a distance-decay relationship in biological wastewater treatment plants? – Xiaohui Wang – Applied and Environmental Microbiology

Microbes in the news

UCSB Professor Wins Bacteria-Killing Grant – Microbial Geneticist David Low Receives Award to Pinpoint BamA Protein – Santa Barbara Independent

Minnesota chief epidemiologist: No cause for concern after anthrax detection
An initial positive test was followed by negative ones, said Dr. Ruth Lynfield. The bacteria can occur naturally. – Beatrice Dupuy – Star Tribune

Master Gardener Explains Soil Nitrogen – Frank Rauchschwalbe – My Mother Lode

US reports first case of bacteria resistant to antibiotic of last resort – The Guardian

May 25, 2016

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The sinonasal microbiome in chronic rhinosinusitis, walnut consumption in a mouse model, and treatment of cows with antibiotics has effects on dung beetle microbiomes.

Jobs and Grants

Assistant professor of food science, microbial ecology – Penn State

American Gastroenterological Association Invites Applications for Gut Microbiome Award – Philanthropy news digest

Three Post-Doctoral Fellowships for Tropical Microbial Ecologists in Panama – Smithsonian Tropical Research Institute

Events

1st International Conference on the Marine Microbiome – Discovery & Innovation for science and industry, 27 June 2016 — 30 June 2016, Berlin, Germany

Pregnancy and birth

Connections between the gut microbiome and metabolic hormones in early pregnancy in overweight and obese women – Luisa F Gomez-Arango – Diabetes

Human oral microbiome

Minireview: A practical guide to the oral microbiome and its relation to health and disease – K Krishnan – Oral Diseases

Human respiratory microbiome

Review: A systematic review of the sinonasal microbiome in chronic rhinosinusitis – Martin Anderson – American Journal of Rhinology & Allergy

Human gut microbiome

Letter: Faecal microbiota profiles as diagnostic biomarkers in primary sclerosing cholangitis – Malte Christoph Rühlemann – Gut

Review: Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children – Evalotte Decker – Gut Microbes

Human vaginal microbiome

Progresses in vaginal microflora physiology and implications for bacterial vaginosis and candidiasis – Gary Ventolini – Women’s Health

Animal experiments

Pulmonary Th17 Antifungal Immunity Is Regulated by the Gut Microbiome – Jeremy P. McAleer – The Journal of Immunology

Microbial modulation of behavior and stress responses in zebrafish larvae – Daniel J. Davis – Behavioural Brain Research

Effects of walnut consumption on colon carcinogenesis and microbial community structure – Masako Nakanishi – Cancer Prevention Research

Animal microbiome

Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata – Sonny T. M. Lee – Frontiers in Microbiology

Free-Living Species of Carnivorous Mammals in Poland: Red Fox, Beech Marten, and Raccoon as a Potential Reservoir of Salmonella, Yersinia, Listeria spp. and Coagulase-Positive Staphylococcus – Aneta Nowakiewicz – PLOS ONE

Treating cattle with antibiotics affects greenhouse gas emissions, and microbiota in dung and dung beetles – Tobin J. Hammer – Proceedings of the Royal Society B

Immune response and gut microbial community structure in bumblebees after microbiota transplants – Kathrin Näpflin – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Effects of consecutive monoculture of Pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing – Linkun Wu – Scientific Reports

Effects of heavy metals and chelants on phytoremediation capacity and on rhizobacterial communities of maize – Giovanni Vigliotta – Journal of Environmental Management

Comparative assessment of fungal augmentation treatments of a fine-textured and historically oil-contaminated soil – Stefano Covino – Science of the Total Environment

Water microbiome

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed – Liyan Song – Microbial Ecology

Built environment microbiome

Review: The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review – Marcus H. Y. Leung – Microbiome

Review: Use of Homogeneously-Sized Carbon Steel Ball Bearings to Study Microbially-Influenced Corrosion in Oil Field Samples – Gerrit Voordouw – Frontiers in Microbiology

Food microbiology

Indigenous Georgian Wine-Associated Yeasts and Grape Cultivars to Edit the Wine Quality in a Precision Oenology Perspective – Ileana Vigentini – Frontiers in Microbiology

Review: Diversity of Microorganisms in Global Fermented Foods and Beverages – Jyoti P. Tamang – Frontiers in Microbiology

Bioinformatics

mockrobiota: a public resource for microbiome bioinformatics benchmarking – Nicholas A Bokulich – PeerJ Preprints

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals – Yevgeny Nikolaichik

Techniques

Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics – Linn Sgie – Nature Communications

Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly – Christopher Huptas – BMC Research Notes

Microbes in the news

Inner Workings: Ancient teeth reveal clues about microbiome evolution – Jyoti Madhusoodanan – PNAS

Study shows cows on antibiotics produce dung with higher levels of greenhouse gases – DW

May 21, 2016

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Helminths positively associated with allergy, baboon vaginal microbiome, nitrogen fixation in poplar trees, boreal lakes as analogues for the Archaean ocean, and PERMANOVA-S as alternative for weighted Unifrac.

Events

2016 Society for Industrial Microbiology and Biotechnology (SIMB) Annual Meeting and Exhibition – July 24-30, New Orleans, LA

General
Editorial overview: Remapping the body of the world: Exploring interactions at the interface of microbial ecology, biological engineering and information science – Steven J. Hallam – Current Opinion in Microbiology

Human oral microbiome

Quantitative molecular detection of 19 major pathogens in the interdental biofilm of periodontally healthy young adults – Florence Carrouel – Frontiers in Microbiology

Species level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population – Nezar Noor Al-hebshi – Journal of Oral Microbiology

Review: Metagenomic Insights into Transferable Antibiotic Resistance in Oral Bacteria – S. Sukumar – Journal of Dental Research

Human gut microbiome

Helminths are positively associated with atopy and wheeze in Ugandan fishing communities: results from a cross-sectional survey – E. L. Webb – Allergy

Stool frequency is associated with gut microbiota composition – Fatemeh Hadizadeh – Gut

The gut-adherent microbiota of PSC–IBD is distinct to that of IBD – Mohammed Nabil Quraishi – Gut

Mucosal adherent bacterial dysbiosis in patients with colorectal adenomas– Yingying Lu – Scientific Reports

Haloferax massiliensis sp. nov., the first human-associated halophilic archaea – Saber Khelaifia – New Microbes and New Infections

Review: The influence of commensal and pathogenic gut microbiota on prion disease pathogenesis – David S. Donaldson – Journal of General Virology

Animal experiments

Effect of Dietary Fibers on Cecal Microbiota and Intestinal Tumorigenesis in Azoxymethane Treated A/J Min/+ Mice – Birgitte Moen – PLOS ONE

Food-grade antimicrobial ɛ-polylysine transiently perturbs the structure of the murine gut microbiome – Xiaomeng You – The FASEB Journal

Animal microbiome

Baboon vaginal microbial flora – Jael A. Obiero – Journal of Medical Primatology

Diversity and fluctuation in ciliate protozoan population in the rumen of cattle – Arfan Abrar – Animal Science Journal

Dietary-driven variation effects on the symbiotic flagellate protist communities of the subterranean termite Reticulitermes grassei Clément – S. Duarte – Journal of Applied Entomology

Plant, root, and soil microbiome

Variable Nitrogen Fixation in Wild Populus – Sharon L. Doty – PLOS ONE

Press: Bacteria in branches naturally fertilize trees – Michelle Ma – University of Washington

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – GigaScience

Conference abstract: Microbial communities associated with the biotransformation potential of insensitive explosives in surface soils – F. Crocker – 2016 SIMB Annual Meeting and Exhibition

Water and extremophile microbiome

Millions of Boreal Shield Lakes can be used to Probe the Evolution of Archaean Ocean Life – Sherry Schiff – bioRxiv

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution – Beatriz Díez – PLOS ONE

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems

Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms – Daniel S Jones – ISME Journal

Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage – Sara Billerbeck – Nature Microbiology

Drinking water, waste and pollution microbiology

Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions – Yingyu Law – Scientific Reports

Conference abstract: Microbial survival in drinking water systems – A. Pinto – 2016 SIMB Annual Meeting and Exhibition

Bioinformatics

PERMANOVA-S: Association test for microbial community composition that accommodates confounders and multiple distances – Zheng-Zheng Tang – Bioinformatics

More microbiology

ppGpp couples transcription to DNA repair in E. coli – Venu Kamarthapu – Science

Press: Factor preserves DNA integrity in bacteria despite assault from antibiotics – Science Daily
Spatial organization shapes the turnover of a bacterial transcriptome – Jeffrey R Moffitt – eLIFE

The Small World Initiative™: An Innovative Crowdsourcing Platform for Antibiotics – Ana Maria Barral – The FASEB Journal

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities – Yinghua Zha – PLOS ONE

Microbes in the news

Featuring my work (but not my quotes): The inner lives of dolphins – Marine mammals carry an unexpected microbial mix – Steve Fyffe – Stanford Medicine Magazine

About Stanley Falkow and Denise Monack: Microbe mentoring: The recipe for success includes independence, a gentle shove and a good stiff drink – Kathy Zonana – Stanford Medicine Magazine

President Obama Awards the National Medals of Science & Technology and Innovation. Stanford Professor of Microbiology Stanley Falkow get his award at 11:30 min in this video.

Students are developing bacteria that eat plastic polluting our oceans. Om nom. – Josh Hrala – Science Alert

A Comprehensive Survey of Preclinical Microbiology Curricula Among US Medical Schools – Dora J. Melber – Clinical Infectious Diseases

University Of California, San Diego Invests $12 Million In Its Own Microbiome Research Efforts! – Vinny – University Herald

Bik’s Picks

Striking Immune Phenotypes in Gene-Targeted Mice Are Driven by a Copy-Number Variant Originating from a Commercially Available C57BL/6 Strain – Vinay S. Mahajan

Press: Immune Defect Detected in Knockout Mice – Tanya Lewis – The Scientist

May 20, 2016

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Updated microbial census, building healthy gut communities, antibiotics might worsen symptoms in transplant patients, another gut-brain connection, and FiveThirtyEight’s Gut Science week.

Events

Bioinformatics for the Microbiome Symposium at Stanford – Friday, May 27

General microbiology

Status of the Archaeal and Bacterial Census: an Update – Patrick D. Schloss – mBio

Suddenly everyone is a microbiota specialist! – Stefan A. Boers – Clinical Microbiology and Infection

Intricacies of assessing the human microbiome in epidemiologic studies – Courtney K. Robinson – Annals of Epidemiology

Pregnancy and birth

Sepsis in preterm infants causes alterations in mucosal gene expression and microbiota profiles compared to non-septic twins – María Cernada – Scientific Reports

From our lab, Editorial: Gut microbiota: How to build healthy growth-promoting gut communities – David A. Relman – Nature Reviews Gastroenterology & Hepatology

Human oral microbiome

Investigating Oral Microbiome Profiles in Children with Cleft Lip and Palate for Prognosis of Alveolar Bone Grafting – Luwei Liu – PLOS ONE

Human skin, eye, and ear microbiome (also see under Animal Experiments below)

Microbiology of Middle Ear Infections: Do You Hear What I Hear? – Donna M. Wolk – Clinical Microbiology Newsletter

Review: Impact of Microbiome on Ocular Health – Abirami Kugadas – The Ocular Surface

Human respiratory microbiome

Azithromycin therapy during RSV bronchiolitis: upper airway microbiome alterations and subsequent recurrent wheeze – Yanjiao Zhou – Journal of Allergy and Clinical Immunology

Human urinary tract microbiome

Research Highlight: Stones: Gut microbiome is unique in kidney stone disease – Rebecca Kelsey – Nature Reviews Urology

Human gut microbiome

Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition – Matthieu Million – Scientific Reports

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease – Steven N. Baldassano – Scientific Reports

Hypothesis: Targeting the Ecology Within: The Role of the Gut-Brain Axis and Human Microbiota in Drug Addiction – Patrick D. Skosnik – Medical Hypotheses

Editorial: FMT — enduring strains – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiota and Metabolic Health: The Potential Beneficial Effects of a Medium Chain Triglyceride Diet in Obese Individuals – Sabri Ahmed Rial – MDPI Nutrients

Fecal Microbiota Transplantation

Predictors of Early Failure After Fecal Microbiota Transplantation for the Therapy of Clostridium Difficile Infection: A Multicenter Study – Monika Fischer – The American Journal of Gastroenterology

Animal experiments

Ly6Chi Monocytes Provide a Link between Antibiotic-Induced Changes in Gut Microbiota and Adult Hippocampal Neurogenesis – Luisa Möhle – Cell Reports

Gut bacteria influence the birth of new brain cells in mice – Jessica Hamzelou – New Scientist

Editorial: Microbiota Alterations in Inflammatory Bowel Diseases: From Correlation to Causality – Benoit Chassaing – CMGH Cellular and Molecular Gastroenterology and Hepatology

Commentary: Canine and Human Atopic Dermatitis: Two Faces of the Same Host-Microbe Interaction – Domenico Santoro – Journal of Investigative Dermatology

Longitudinal Evaluation of the Skin Microbiome and Association with Microenvironment and Treatment in Canine Atopic Dermatitis – Charles W. Bradley – Journal of Investigative Dermatology

Plant, root, and soil microbiome

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain) – Gema Bárcenas-Moreno – Science of The Total Environment

Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis – Ning Ling – Soil Biology and Biochemistry

Mycorrhiza and heavy metal resistant bacteria enhance growth, nutrient uptake and alter metabolic profile of sorghum grown in marginal soil – Faten Dhawi – Chemosphere

Built environment microbiome

Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures – D. Vázquez-Nion

Pollution and waste microbiology

Microbial diversity and community structure in an antimony-rich tailings dump – Enzong Xiao – Applied Microbiology and Biotechnology

Food microbiology

A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model – Amélie Rouger – International Journal of Food Microbiology

Bioinformatics, proteomics, metabolomics

An adaptive association test for microbiome data: R package MiSPU – Chong Wu – Genome Medicine

Review: The information science of microbial ecology – Aria S Hahn – Current Opinion in Microbiology

Editorial: Proteomic interrogation of the gut microbiota: potential clinical impact – Sven-Bastiaan Haange – Expert Review of Proteomics

Microbial community metabolic modeling: A community data-driven network reconstruction – Christopher S. Henry – Journal of Cellular Physiology

More microbiology

Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice – Yusuke Shono – Science Translational Medicine

Some antibiotics may worsen complications in transplant patients – Science Daily

Microbes in the news

Welcome To FiveThirtyEight’s Gut Science Week – Maggie Koerth-Baker

Everybody Is Constipated, Nobody Is Constipated – Maggie Koerth-Baker

What Your Poop Says About You – Christine Laskowski

Probiotics Won’t Fix All Your Health Problems – Katherine Hobson

What Your Poop Says About You – Christine Laskowski

Is Gut Science Biased? – Anna Maria Barry-Jester

How Your Gut Affects Your Mood – Christie Aschwanden – FiveThirtyEight

Your Mouth Has Bacteria “That Could Grow on Mars,” Says a NASA Scientist – Especially if you had cheese sometime recently – Neel V. Patel – Inverse

Science, publishing, and career

Preprints for the life sciences – Jeremy M. Berg – Science

May 19, 2016

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Two papers on triclosan effects, genome reduction in a common soil bacterium, spatial patterns of ocean microbes, and deep sequencing in unexplained fever cases.

Triclosan and microbiome

Two very different papers about the effect of triclosan on the microbiome:

Crossover Control Study of the Effect of Personal Care Products Containing Triclosan on the Microbiome – Angela C. Poole – mSphere

Antimicrobial in Common Toothpaste Doesn’t Impact Gut, Oral Microbiome – ASM

but:

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish – Christopher A. Gaulke – PLOS ONE

The Case Against Antibacterial Soap Is Getting Stronger – Alexandra Sifferlin – Time

Human oral microbiome

Undergraduate thesis: Exploring a possible correlation between the human oral microbiome and body mass index – Ivy S. McDermot – University of Colorado Boulder

Human gut microbiome

Irritable Bowel Syndrome special in Nature: 
Irritable bowel syndrome – Michelle Grayson
Microbiome: Bacterial broadband – Michael Eisenstein

HIV infection results in metabolic alterations in the gut microbiota different from those induced by other diseases – Sergio Serrano-Villar – Scientific Reports

Review: The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni – Therapeutic Advances in Gastroenterology

Animal experiments

Microbiome-metabolome responses in the cecum and colon of pig to a high resistant starch diet – Yue Sun – Frontiers in Microbiology

Animal microbiome

Characterisation of the bacterial community structures in the intestine of Lampetra morii – Yingying Li – Antonie van Leeuwenhoek

Review: Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications – R.M. Stumpf – Biological Conservation

Plant, root, and soil microbiome

Genome reduction in an abundant and ubiquitous soil bacterial lineage – Tess Brewer – bioRxiv

Insight into structure dynamics of soil microbiota mediated by the richness of replanted Pseudostellaria heterophylla – Yong-Po Zhao – Scientific Reports

Review: Microbial inoculation of seed for improved crop performance: issues and opportunities – Maureen O’Callaghan – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Distinct Spatial Patterns of SAR11, SAR86, and Actinobacteria Diversity along a Transect in the Ultra-oligotrophic South Pacific Ocean – Nyree J. West – Frontiers in Microbiology

In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)—A Unique Microbial Habitat – Erik C. L. Trampe – Frontiers in Microbiology

Waste and pollution microbiology

Diversity of ammonia-oxidizing bacteria and archaea in response to different aeration rates during cattle manure composting – Lei Yan – Ecological Engineering

Microbes and infection

Deep sequencing approach for investigating infectious agents causing fever – T. N. Susilawati – European Journal of Clinical Microbiology & Infectious Diseases

Metagenomics and bioinformatics

A two-part mixed-effects model for analyzing longitudinal microbiome compositional data – Eric Z. Chen – Bioinformatics

Review: Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis – Vanessa Aguiar-Pulido, Wenrui Huang, Victoria Suarez-Ulloa, Trevor Cickovski, Kalai Mathee and Giri Narasimhan – Evolutionary Bioinformatics

More microbiology

Structure of the T4 baseplate and its function in triggering sheath contraction – Nicholas M. I. Taylor – Nature

How viruses infect bacteria: A tale of a tail – EurekAlert

A platform for the discovery of new macrolide antibiotics – Ian B. Seiple – Nature

Microbes in the news

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters
University of South Florida Scientists Discover Antarctic Sponge Extract Can Help Kill MRSA – University of South Florida
Arctic Sponge Extract May Be Potent Against MRSA – Xuan Pham – Lab Roots

These bacteria are all over your wallet and smartphone
“Due to rising temperatures, we will NOT be accepting boob or sock money.” – Maria Lamagna – MarketWatch

Tampa Bay: Bacteria threatens Bay Area palm trees #Phytoplasma

Panda poop study provides insights into microbiome, reproductive troubles – EurekAlert

Indian gut similar to Bangladeshis, omnivorous animals, claims study
We acquire them from our mothers during birth, pass on to us through the breast milk and live with us till we die – Anuradha Mascarehnas – Indian Express

Science, publishing, and career

Ecology: The sea-otter whisperer – Jane Lubchenco – Nature

Bik’s Picks

MinION in space: Virologist Kate Rubins is set to make history as the first person to sequence DNA in space – Frontline Genomics

With lighting by my husband’s company Xicato: Arts: California on camera. The re-opening of the San Francisco Museum of Modern Art – John Gilbey – Nature