Author Archives: bergmaureen

August 10, 2017

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Human urinary microbiome

The microbiome in urogenital schistosomiasis and induced bladder pathologies – Adewale S. Adebayo – PLoS Negl Trop Dis

Human gut microbiome

A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes – Lena Takayasu – PLoS ONE

Plant, root, and soil microbiome

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence – Yun Kit Yeoh – Nature Communications

Spatiotemporal Variation and Networks in the Mycobiome of the Wheat Canopy – Rumakanta Sapkota – Frontiers in Plant Science

Water and extremophile microbiome

Active microorganisms thrive among extremely diverse communities in cloud water – Pierre Amato – PLoS ONE

Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan – Satoshi Hiraoka – Frontiers in Microbiology

Built environment

The US National Mall Microbiome: A Census of Rhizosphere Bacteria Inhabiting Landscape Turf – Jo Anne Crouch – Crop Science

Microbes in the news

For Healthy Skin, Just Add…Bacteria? – Adam Hurly – GQ

Microbes on the market

Reality vs. hype: A macro look at the microbiome market – Juliet Preston – MedCityNews

Science, publishing, and career

Prof claims victory over ‘#manel’ at microbiome conference – Dan Jackson – Campus Reform

August 9, 2017

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Events and jobs

ASM Journals Fellowship – American Society for Microbiology

General microbiome

A mechanistic Individual-based Model of microbial communities – Pahala Gedara Jayathilake – PLoS ONE

Human vaginal microbiome

Group B Streptococcus and the vaginal microbiota – Geoffrey H Rosen – The Journal of Infectious Diseases

Animal experiments

The microbial metabolite desaminotyrosine protects from influenza through type I interferon – Ashley L. Steed – Science

Development of Inflammatory Bowel Disease is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – bioRxiv

Plant, root, and soil microbiome

Microbial Communities as Ecological Indicators of Ecosystem Recovery Following Chemical Pollution – Stéphane Pesce – Microbial Ecotoxicology

Assessment of rhizosphere processes for removing water-borne macrolide antibiotics in constructed wetlands – Yiping Tai – Plant and Soil

Poor-Soil Rhizosphere Enriched with Different Microbial Activities Influence the Availability of Base Elements – Faten Dhaw – Open Journal of Ecology

Water and extremophile microbiome

Impacts of leachates from livestock carcass burial and manure heap sites on groundwater geochemistry and microbial community structure – Man Jae Kwon – PLoS ONE

Built environment

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity – Emma Ransom-Jones – mSphere

Probiotics / prebiotics

Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (Gallus gallus domesticus) during Downstream Poultry Processing – Vamsy Priya Guttala – Agricultural Sciences

Lactobacillus casei CCFM419 attenuates type 2 diabetes via a gut microbiota dependent mechanism – Gang Wang – Food & Function

Bioinformatics

Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information – Albert Barberán – mSphere

Techniques

Isolation of bacteriophages from air using vacuum filtration technique: An improved and novel method – Bhagyashree Magare – Journal of Applied Microbiology

Microbes in the news

Exploring the Equine Microbiome – Stacey Oke – The Horse

Study: Kitchen sponges carry more bacteria than a toilet – Darren Sweeney – Fox8 Cleveland

July 14, 2017

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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

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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

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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

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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

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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

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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

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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

April 8, 2017

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General microbiome

Modeling The Consequences Of Heterogeneity In Microbial Population Dynamics – Helena Herrmann – BioRxiv

Human respiratory microbiome

16S rRNA Gene Sequencing Reveals Site-Specific Signatures Of The Upper And Lower Airways Of Cystic Fibrosis Patients – Sarah K. Lucas – BioRxiv

Review: Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment? – Kian Fan Chung – The Journal of Allergy and Clinical Immunology

Human skin microbiome

Toxification of polycyclic aromatic hydrocarbons by commensal bacteria from human skin – Juliane Sowada – Archives of Toxicology

Human gut microbiome

Long-term use of antibiotics and risk of colorectal adenoma – Yin Cao – Gut

Changes in Composition of the Gut Bacterial Microbiome after Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in a Pediatric Heart Transplant Patient – Kyle L. Flannigan – Frontiers in Cardiovascular Medicine

Animal experiments

Iron Supplements Modulate Colon Microbiota Composition and Potentiate the Protective Effects of Probiotics in Dextran Sodium Sulfate-induced Colitis – Marco Constante – Inflammatory Bowel Diseases

Animal microbiome

Intestinal microbiota of healthy and unhealthy Atlantic salmon Salmo salar L. in a recirculating aquaculture system – Chun Wang – Chinese Journal of Oceanology and Limnology

Identification and modes of action of endogenous bacteria in taphonomy of embryos and larvae – Justin L. Eagan – Palaios

Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity – Yan Zeng – AMB Express

Skin microbiota differs drastically between co-occurring frogs and newts – Molly C. Bletz – The Royal Society Open Science

Amphibian skin microbiota exhibits temporal variation in community structure but stability of predicted Bd-inhibitory function – Molly C Bletz – ISME

Plant, root, and soil microbiome

Characterization of a metagenome-derived protease from contaminated agricultural soil microorganisms and its random mutagenesis – Chengjian Jiang – Folia Microbiologica

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests – Luis E Castañeda – PeerJ

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates – Suchismita Ghosh – BMC Microbiology

Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria – Nagissa Mahmoudi – Environmental Microbiology

Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China – Bo Xu – Biogeosciences

Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration – Deepak Kumaresan – Scientific Reports

Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems – P. Trivedi – Soil Biology and Biochemistry

Water and extremophile microbiome

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater – William B. Ludington – PLOS ONE

Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i – Heather Fullerton – ISME

Performance and microbial community analysis in a modified anaerobic inclining-baffled reactor treating recycled paper mill effluent – Haider M. Zwain – Environmental Science and Pollution Research

Microbial formation of labile organic carbon in Antarctic glacial environments – H. J. Smith – Nature Geoscience

Review: Cryospheric science: The power of glacial microbes – Elizabeth B. Kujawinski – Nature Geoscience

Taxonomic composition of Lake Baikal bacterioneuston communities – A. D. Galach’yants – Microbiology

Performance and microbial population dynamics during stable operation and reactivation after extended idle conditions in an aerobic granular sequencing batch reactor – Qiulai He – Bioresource Technology

Comparative metagenomics reveals insights into the deep-sea adaptation mechanism of the microorganisms in Iheya hydrothermal fields – Hai-liang Wang – Journal of Marine Systems

Built environment

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City – Julia M. Maritz – PLOS ONE

Food microbiology

The Dynamic Microbiota Profile During Pepper (Piper nigrum L.) Peeling by Solid-State Fermentation – Qisong Hu – Current Microbiology

Molecular investigation of bacterial communities during the manufacturing and ripening of semi-hard Iranian Liqvan cheese – M. Ramezani – Food Microbiology

Identification of microbial communities, with a focus on foodborne pathogens, during kimchi manufacturing process using culture-independent and -dependent analyses – Hae-Won Lee – LWT – Food Science and Technology

Probiotics / prebiotics

Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial – Judit Villar-García – PLOS ONE

Phages and viruses

Taxonomic variability and functional stability in microbial communities infected by phages – Stilianos Louca – Environmental Microbiology

Bioinformatics

EzMap: A Simple Pipeline for Reproducible Analysis of the Human Virome – Patrick Czeczko – Bioinformatics

Microbes in the news

You Should Appreciate Germs – Bill Gates

Microbes on the market

The expanding ecosystem of microbiome startups – Juliet Preston – MedCity News