July 14, 2017

Events and jobs

Postdoc, Lieberman Lab

General microbiome

Assembly of Microbial Communities in Replicate Nutrient-Cycling Model Ecosystems Follows Divergent Trajectories, Leading to Alternate Stable States – Eulyn Pagaling – Environmental Microbiology

Human respiratory microbiome

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome – Marion Engel – PLOS ONE

Human gut microbiome

Gut bacterial peptides with autoimmunity potential as environmental trigger for late onset complex diseases: In–silico study – Sapna Negi – PLOS ONE

Impact of environmental microbiota on human microbiota of workers in academic mouse research facilities: An observational study – Peggy S. Lai – PLOS ONE

Reduced Mass and Diversity of the Colonic Microbiome in Patients with Multiple Sclerosis and Their Improvement with Ketogenic Diet – Alexander Swidsinski – Frontiers in Microbiology

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls – Christopher J. Stewart – Microbiome

Other Human microbiome

The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries – Apoena Aguiar Ribeiro – PLOS ONE

The oral fungal mycobiome: characteristics and relation to periodontitis in a pilot study – Brandilyn A. Peters – BMC Microbiology

Animal experiments

Three distinct pneumotypes characterize the microbiome of the lung in BALB/cJ mice – Julia Scheiermann – PLOS ONE

Assessment of gut microbiota populations in lean and obese Zucker rats – Reza Hakkak – PLOS ONE

Preparing the Gut with Antibiotics Enhances Gut Microbiota Reprogramming Efficiency by Promoting Xenomicrobiota Colonization – Shou K. Ji – Frontiers in Microbiology

Animal microbiome

On the core bacterial flora of Ixodes persulcatus (Taiga tick) – Shuo Sui – PLOS ONE

Skin microbiota in frogs from the Brazilian Atlantic Forest: Species, forest type, and potential against pathogens – Ananda Brito de Assis – PLOS ONE

Brackish habitat dictates cultivable Actinobacterial diversity from marine sponges – Gregory A. Ellis – PLOS ONE

Effects of Kluyveromyces marxianus supplementation on immune responses, intestinal structure and microbiota in broiler chickens – Weiwei Wang – PLOS ONE

Dominance-function relationships in the amphibian skin microbiome – Jenifer B. Walke – Environmental Microbiology

Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis – J.N.Cullen – Veterinary Microbiology

Bacterial community composition in Adélie (Pygoscelis adeliae) and Chinstrap (Pygoscelis antarctica) Penguin stomach contents from Signy Island, South Orkney Islands – W. C. Yew – Polar Biology

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows – Ilma Tapio – PLOS ONE

Honeybee (Apis mellifera)-associated bacterial community affected by American foulbrood: detection of Paenibacillus larvae via microbiome analysis – Tomas Erban – Scientific Reports

Plant, root, and soil microbiome

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium – Arthur Prudêncio de Araujo Pereira – PLOS ONE

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth – Heather C. Manching – bioRxiv

Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface – Lily Momper – Environmental Microbiology Reports

Patterns of soil bacterial richness and composition tied to plant richness, soil nitrogen, and soil acidity in alpine tundra – Xia Yuan – Arctic, Antarctic, and Alpine Research

Water and extremophile microbiome

Unravelling riverine microbial communities under wastewater treatment plant effluent discharge in large urban areas – Yang Huo – Applied Microbiology and Biotechnology

Phages and viruses

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans – Felipe H. Coutinho – Nature Communications

Science, publishing, and career

Jonathan Eisen named Faculty Director of the UC Davis Microbiome Initiative

June 28, 2017

Human vaginal microbiome

Vaginal seeding or vaginal microbial transfer from the mother to the cesarean born neonate: a commentary regarding clinical management – Thor Haahr – BJOG

Human gut microbiome

*Review: The resilience of the intestinal microbiota influences health and disease – Felix Sommer – Nature Reviews Microbiology

Other human microbiome

Urinary catheter-associated microbiota change in accordance with treatment and infection status – Laetitia Bossa – PLOS ONE

Dynamics of the Oral Microbiota as a Tool to Estimate Time Since Death – Joe Adserias Garriga – Molecular Oral Microbiology

Animal experiments

Tuftsin-Phosphorylcholine maintains normal gut microbiota in collagen induced arthritic mice – Hila Ben-Amram – Frontiers in Microbiology

Animal microbiome

The Diet and Gut Microbial Communities of Two Closely Related Combtooth Blennies, Chasmodes saburrae and Scartella cristata – Peter J. Hundt – Copeia

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair R. Legione – bioRxiv

Plant, root, and soil microbiome

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome – Luhua Yang – Frontiers in Plant Science

Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing – Honghong Guo – Ecotoxicology and Environmental Safety

Root Hair Mutations Displace the Barley Rhizosphere Microbiota – Senga Robertson-Albertyn – Frontiers in Plant Science

*Review: Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere – Franciska T. de Vries – Journal of Ecology

Rhizosphere microorganisms affected by soil solarization and cover cropping in Capsicum annuum and Phaseolus lunatus agroecosystems – Nancy Kokalis-Burelle – Applied Soil Ecology

Bacterial community dynamics in the rhizosphere of a long-lived, leguminous shrub across a 40-year age sequence – Xiaofan Na – Journal of Soils and Sediments

Microbial populations of stony meteorites: Substrate controls on first colonisers – Alastair W. Tait – Frontiers in Microbiology

Water and extremophile microbiome

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage – Wenkai Teng – Minerals

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer – Donald Pan – Frontiers in Microbiology

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat – Jackson Z Lee – bioRxiv

Bioinformatics

Mixed Effect Dirichlet-Tree Multinomial for Longitudinal Microbiome Data and Weight Prediction – Yunfan Tang – arXiv

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project – James B. Pettengill – PeerJ

Techniques

Assembly and Tracking of Microbial Community Development within a Microwell Array Platform – Andrea C. Timm – JOVE

June 6, 2017

Short digest today!
Events and jobs

R&D Scientist (Microbiome) – USANA – Salt Lake City, UT

Human respiratory microbiome

Temporal changes in the nasal microbiota and host antimicrobial responses to intranasal mupirocin decolonisation: Observations in healthy staphylococcal carriers – Su-Hsun Liu – bioRxiv

Plant, root, and soil microbiome

Coordinated responses of soil communities to elevation in three subarctic vegetation types – G. F. (Ciska) Veen – Oikos

Water and extremophile microbiome

Impact of ferrous iron on microbial community of the biofilm in microbial fuel cells – Qian Liu – Frontiers in Microbiology

The deep-sea microbial community from the Amazonian Basin associated with oil degradation – Mariana E. Campeão – Frontiers in Microbiology

Microbial community structure of deep-sea hydrothermal vents on the ultraslow spreading Southwest Indian Ridge – Jian Ding – Frontiers in Microbiology

Draft Genome Sequences of Thermophiles Isolated from Yates Shaft, a Deep-Subsurface Environment – Nitin K. Singh – Genome Announcements

Phages and viruses

Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics – Paloma S. Moreno – PLOS ONE

Microbes in the news

Microbe from Yogurt Impedes Drug-Resistant Bacteria – Aggie Mika – The Scientist

May 13, 2017

Events and jobs

Microbiology/Molecular Biology/Wildlife Disease Technician: Wisconsin – USGS – National Wildlife Health Center

Sr. Associate, Quality Control Microbiology – Moderna

Staff Research Associate, Anaerobic Microbiology – UC Berkeley

General microbiome

Perspective: The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals – Alfredo Franco-Obregón – mSystems

Human gut microbiome

Systemic sclerosis is associated with specific alterations in gastrointestinal microbiota in two independent cohorts – Elizabeth R Volkmann – BMJ Open Gastroenterology

Review: Microbiota: Clostridia protect from gut infections in early life – Irene Vacca – Nature Reviews Microbiology

Animal microbiome

The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures – Stéphanie Céline Michl – PLOS ONE

Plant, root, and soil microbiome

Bacterial root microbiome of plants growing in oil sands reclamation covers – Eduardo Kovalski Mitter – Frontiers in Microbiology

Effect of Trichoderma harzianum on maize rhizosphere microbiome and biocontrol of Fusarium Stalk rot – Kandasamy Saravanakumar – Scientific Reports

Water and extremophile microbiome

Characterisation of Arctic Bacterial Communities in the Air above Svalbard – Lewis Cuthbertson – Biology

Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island – Garabed Antranikian – Extremophiles

Unique and highly variable bacterial communities inhabiting the surface microlayer of an oligotrophic lake – Mylène Hugoni – Aquatic Microbial Ecology

Distribution and activity of benthic bacteria in four lakes in the Bory Tucholskie National Park (Poland) – Łukasz Kubera – Aquatic Microbial Ecology

Role of EPS, Dispersant and Nutrients on the Microbial Response and MOS Formation in the Subarctic Northeast Atlantic – Laura Duran Suja – Frontiers in Microbiology

Food microbiology

Impact of a Microbial Cocktail Used as a Starter Culture on Cocoa Fermentation and Chocolate Flavor – Igor Magalhães da Veiga Moreir – Molecules

Techniques

Harnessing the power of digital droplet PCR to conduct real-world microbial competitions – Helen A. Murphy – Molecular Ecology Resources

Microbes in the news

Lung microbiome – Sally Robertson – News-Medical.Net

Resistant Starch from Potatoes Offers Benefits to Gut Microbiome? – Michael Crane – Nutritional Outlook

Visualizing the Microbiome through Handmade Embroidery – Clara Rodríguez Fernández – labiotech

Microbes on the market

‘Imagine being able to edit the microbiome’ – TechAccel talks animal nutrition targeted innovation – Aerin Einstein-Curtis – Feed Navigator

Science, publishing, and career

Weill Cornell Aims For ‘Precision Metagenomics’ With Quantitative Computing – Neil Versel – GenomeWeb

May 6, 2017

Events and jobs

Trainee Microbiology Analyst – Eurofins Lancaster Laboratories

General microbiome

*Review: Optimizing methods and dodging pitfalls in microbiome research – Dorothy Kim – Microbiome

*Book: Dirt Is Good: The Advantage of Germs for Your Child’s Developing Immune System – Jack Gilbert, Rob Knight

Human gut microbiome

*Review: Ménage à trois in the human gut: interactions between host, bacteria and phages – Mohammadali Khan Mirzaei – Nature Reviews Microbiology

Animal microbiome

The functional microbiome of arthropods – Mauro Degli Esposti – PLOS ONE

A comparative study of gut microbiota profiles of earthworms fed in three different substrates – Dianfeng Liu – Symbiosis

Plant, root, and soil microbiome

Breaking continuous potato cropping with legumes improves soil microbial communities, enzyme activities and tuber yield – Shuhao Qin – PLOS ONE

Study on the effect of soil beneficial microorganisms on the growth of kiwifruit – Huihe Li – Biomedical Research

Water and extremophile microbiome

Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons – Jérôme Comte – Environmental Microbiology

*Review: The life sulfuric: microbial ecology of sulfur cycling in marine sediments – Kenneth Wasmund – Environmental Microbiology Reports

Fine stratification of microbial communities through a metagenomic profile of
the photic zone – Jose M. Haro-Moreno – bioRxiv

Probiotics / prebiotics

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens – Alessandra De Cesare – PLOS ONE

Bioinformatics

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation – CC Laczny – Nucleic Acids Research

Techniques

*Highlight: How to see more: double hybridization to reveal ecological differentiation among close bacterial relatives – Stefan Bertilsson – Environmental Microbiology

Comparative analysis of the sensitivity of metagenomic sequencing and PCR to detect a biowarfare simulant (Bacillus atrophaeus) in soil samples – Delphine Plaire – PLOS ONE

Microbes in the news

The Invisible Secret That Will Change Your Skin Forever – Rachel Krause – Refinery29

Improve your skin microbiome – Cassie Shortsleeve – Furthermore

Dormant bacteria trapped in ice could be released by climate change – Alayna Treene – Axios

Microbes on the market

Commense Licenses UBC’s Microbiome Therapeutic for Preventing Childhood Asthma – Genetic Engineering & Biotechnology News

Bacteria Hysteria

Why Bacteria Are More Threatening Than Ever – Alice Park – Time

Science, publishing, and career

Infection and Immunity welcomes the new microbiology – Andreas J. Bäumler – Infection and Immunity

April 29, 2017

Events and jobs

Bioinformatics Scientist, Microbiome – Human Longevity Inc.

General microbiome

The hologenome across environments and the implications of a host-associated microbial repertoire – Tyler J. Carrier – Frontiers in Microbiology

Teleosts as Model Organisms to Understand Host-Microbe Interactions – Emily A. Lescak – Journal of Bacteriology

*Review: The Shifting Microbiome in Surgical Stress – Panna A. Codner – Current Surgery Reports

A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations – Marie Marchal – BMC Evolutionary Biology

Human gut microbiome

Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome – Dorottya Nagy-Szakal – Microbiome

Study protocol on the role of intestinal microbiota in colorectal cancer treatment: a pathway to personalized medicine 2.0 – R. Aarnoutse – International Journal of Colorectal Disease

Animal experiments

Differences in microbiota membership along the gastrointestinal tract of piglets and their differential alterations following an early-life antibiotic intervention – Chunlong Mu – Frontiers in Microbiology

Animal microbiome

Biogeographic comparison of Lophelia-associated bacterial communities in the western Atlantic reveals conserved core microbiome – Christina A. Kellogg – Frontiers in Microbiology

Plant, root, and soil microbiome

Response of methanogenic microbial communities to desiccation stress in flooded and rain-fed paddy soil from Thailand – Andreas Reim – Frontiers in Microbiology

Metagenomics of Microbial Communities Associated with the Rhizosphere of the Saudi Desert Medicinal Plants – Mohammed N Baeshen – EC Microbiology

Rhizospheric soil enzyme activities and phytominimg potential of Aeluropus lagopoides and Cyperus conglomeratus growing in contaminated soils at the banks of artificial lake of reclaimed wastewater – Zahid Khorshid Abbas – International Journal of Phytoremediation

*Review: The unseen rhizosphere root-soil-microbe interactions for crop production – Ruifu Zhang – Current Opinion in Microbiology

Water and extremophile microbiome

Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments – Marion H. Stagars – Frontiers in Microbiology

Novel large sulfur bacteria in the metagenomes of groundwater-fed chemosynthetic microbial mats in the Lake Huron basin – Allison M. Sharrar – Frontiers in Microbiology

Microbial population dynamics and ecosystem functions of anoxic/aerobic granular sludge in sequencing batch reactors operated at different organic loading rates – Enikö Szabó – Frontiers in Microbiology

Characteristics of bacterial community in cloud water at Mt Tai: similarity and disparity under polluted and non-polluted cloud episodes – Min Wei – Atmospheric Chemistry and Physics

Built environment

Density assessment and mapping of microorganisms around a biocomposting plant in Sanandaj, Iran – Sanaz Rashidi – Environmental Monitoring and Assessment

Techniques

High throughput and quantitative measurement of microbial metabolome by gas chromatography/mass spectrometry using automated alkyl chloroformate derivatization – Linjing Zhao – Analytical Chemistry

Functional Association Prediction by Community Profiling – Dazhi Jiao – Methods

*Book: Modern Tools and Techniques to Understand Microbes – Ajit Varma

Microbes on the market

Microbiome market competitive landscape technology in 2017 pipeline review published by leading research firm – WhaTech

Science, publishing, and career

Review of 3rd annual Translation Microbiome Conference – James Vitale – Taconic

April 22, 2017

General microbiome

The Microbiome – The Biochemist (full issue)

Human vaginal microbiome

*Review: What fertility specialists should know about the vaginal microbiome: a review – Juan Antonio García-Velascoa – Reproductive BioMedicine Online

Animal experiments

Microbiota-Induced Antibodies Are Essential for Host Inflammatory Responsiveness to Sterile and Infectious Stimuli – Daniel Cisalpino – Journal of Immunology

Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans – Timothy A. Scott – Cell

Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics – Aurian P. García-González – Cell

Examining the role of the microbiome in the effectiveness of colorectal cancer treatment – Jim Fessenden – UMass Medical School Communications

Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens – Yun-Gi Kim – Science

Infant mice lack microbes that help fight intestinal infection – EurekAlert!

Effects of different oligosaccharides at various dosages on the composition of gut microbiota and short-chain fatty acids in mice with constipation – Linlin Wang –  Food & Function

Short Term High Fat Diet Induces Obesity-Enhancing Changes in Mouse Gut Microbiota That are Partially Reversed by Cessation of the High Fat Diet – Yue Shang – Lipids

Animal microbiome

Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature – Andrian P. Gajigan – Microbiology Open

Characterization of the gut microbiota in the golden takin (Budorcas taxicolor bedfordi) – Jun Chen – AMB Express

*Opinion: Mammary microbiota of dairy ruminants: fact or fiction? – Pascal Rainard – Veterinary Research

Determination of the microbial community features of Haemaphysalis flava in different developmental stages by high-throughput sequencing – Deyong Duan – Journal of Basic Microbiology

Plant, root, and soil microbiome

A signature of tree health? Shifts in the microbiome and the ecological drivers of horse chestnut bleeding canker disease – Britt Koskella – New Phytologist

Soil aggregates as massively concurrent evolutionary incubators – Matthias C Rillig – ISME

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment – Qing Wang – Biology and Fertility of Soils

*Editorial: Signalling in the phytomicrobiome: Understanding and harnessing the plant holobiont – Donald L. Smith – Frontiers in Plant Science

Warming enhances old organic carbon decomposition through altering functional microbial communities – Lei Cheng – ISME

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Long-term straw returning affects Nitrospira-like nitrite oxidizing bacterial community in a rapeseed-rice rotation soil – Xuesong Luo – Journal of Basic Microbiology

Water and extremophile microbiome

Attenuation and modification of the ballast water microbial community during voyages into the Canadian Arctic – Mattias L. Johansson – Diversity and Distributions

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms – Inga Leena Angell – Letters in Applied Microbiology

*Review: The life sulfuric: Microbial ecology of sulfur cycling in marine sediments – Kenneth Wasmund – Environmental Microbiology Reports

Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra – Enrique Zozaya-Valdés – Environmental Microbiology

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds – Christian Wurzbacher – ISME

Built environment

Diversity changes of microbial communities into hospital surface environments – Rika Yano – Journal of Infection and Chemotherapy

Bioinformatics

A Robust Symmetric Nonnegative Matrix Factorization Framework for Clustering Multiple Heterogeneous Microbiome Data – Yuanyuan Ma – Preprints

Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline – Daniel J. White – Journal of Computational Biology

Techniques

Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut – Bentley Lim – Cell

‘Genetic scalpel’ can manipulate the microbiome, Yale study shows – Bill Hathaway – Yale News

What is broad-range 16S rDNA PCR? – Amani Patel – Microbiology and Infectious Disease

Microbes in the news

Microbiome: The Body’s Great Conductor –  Conan Milner – Epoch Times

Our Gut Microbes Have Circadian Rhythms, Too — And They Might Own Us – Jesslyn Shields – HowStuffWorks

The Bacteria That Can Help Find Land Mines – Daniel Akst – The Wall Street Journal

Science, publishing, and career

Grant Addresses Computational Challenges in Microbiome Research – Jacobs School of Medicine and Biomedical Science