May 17, 2017

Today’s digest includes a few studies of the interactions between microbes (and synergy in metabolism and other processes), a filling of human gut microbiology, and interesting insights into probiotics both in animals and humans.  Also, check out my post later in the day reviewing microbiome related talks at BioData World West 2017 (late April)

Events and jobs

Scientist – Microbiomics – ZymoResearch

PhD in microbiology – Université Catholique de Louvain (UCL)

Microbiology Laboratory Technologist – Yukon Hospital Corporation – Whitehorse, YT

General microbiome

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities – Margaret F Romine – The ISME Journal

Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation – Sarah M. Douglas – PLOS ONE

Pregnancy and early life

PrePrint – Gut dysbiosis following C-section instigates higher colonisation of toxigenic Clostridium perfringens in infants – Nagpal R – Benef Microbes

The influence of dietary immunomodulatory factors on development of food allergy in children – Sardecka I – Postepy Dermatol Alergol.

 

Human oral microbiome

The microbiome of site-specific dental plaque of children with different caries status – Richards VP – Infection and Immunity

Human gut microbiome

Healthy gut microbiota can resolve undernutrition – Emmanuel Hermann – HBSN

The Gut Microbiota and Autism Spectrum Disorders – Qinrui Li – Frontiers in Cellular Neuroscience

The ecological community of commensal, symbiotic, and pathogenic gastrointestinal microorganisms – an appraisal – Haque SZ – Dovepress

Comparative Effectiveness of Faecal Microbiota Transplant by Route of Administration – Nathan D. Gundacker – The Journal of Hospital Infection

Fecal microbiota transplantation in recurrent Clostridium difficile infection in a patient with concomitant inflammatory bowel disease – Gravito-Soares M – Rev Esp Enferm Dig

Alterations in intestinal microbiota relate to intestinal failure-associated liver disease and central line infections – Panliang Wang – Journal of Pediatric Surgery

* The Gastric Microbiome and Its Influence on Gastric Carcinogenesis: Current Knowledge and Ongoing Research – Chao Zhang – Hematology/Oncology Clinics of North America

Insights into the role of the intestinal microbiota in colon cancer – Oke S – Therapeutic Advances in Gastroenterology

Gut microbiota changes as a risk factor for obesity – Kvit KB – Wiad Lek.

Animal experiments 

Drosophila melanogaster as a High-Throughput Model for Host–Microbiota Interactions – Mark Trinder – Frontiers in Microbiology

Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice – Guiping Guan – Mediators of Inflammation

Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 2. Effects of gastrointestinal site and age – J.J. Castro – Journal of Dairy Science

The microbiome regulates amygdala-dependent fear recall – Hoban AE – Molecular Psychiatry

Animal microbiome

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

The influence of a probiotic supplementation on memory in quail suggests a role of gut microbiota on cognitive abilities in birds – Severine Parois – Behavioural Brain Research

Gut microbial communities of American pikas (Ochotona princeps): evidence for phylosymbiosis and adaptations to novel diets – Kevin D. Kohl – Journal of Animal Ecology

This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth-Microbiota Interactions in Veterinary Species – Peachey LE – Trends in Parasitology

Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes – Baldo L – ISME

Plant, root, and soil microbiome

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – The ISME Journal

Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse – Chol Gyu Lee – Microbes and Environments

Water and extremophile microbiome

Annual community patterns are driven by seasonal switching between closely related marine bacteria – Christopher S Ward – The ISME Journal

A bacterial community-based index to assess the ecological status of estuarine and coastal environments – Eva Aylagas – Marine Pollution Bulletin

The impact of wastewater treatment effluent on microbial biomasses and diversities in coastal sediment microcosms of Hangzhou Bay – Yile Tao – Marine Pollution Bulletin

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats – Johanne Aubé – Marine Pollution Bulletin

Changes in microbial community during hydrogen and methane production in two-stage thermophilic anaerobic co-digestion process from biowaste – S. Zahedi – Waste Management

Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India – Chaudhuri B – Genomics Data

Built environment (subways, indoor surfaces)

Characterizing bacterial communities in paper production-troublemakers revealed – Zumsteg A – MicrobiologyOpen

 

Probiotics / prebiotics

Dairy Propionibacteria: Versatile Probiotics – Rabah H – Microorganisms

Contribution of anthocyanin-rich foods in obesity control through gut microbiota interactions – Jamar G – BioFactors

Positive Effect of Probiotics on Constipation in Children: A Systematic Review and Meta-Analysis of Six Randomized Controlled Trials – Huang R – Frontiers in Cellular and Infection Microbiology

Mechanisms of Action of Probiotics and the Gastrointestinal Microbiota on Gut Motility and Constipation – Dimidi E – Advances in Nutrition

Bioinformatics

PrePrint – MetaMeta: Integrating Metagenome Analysis Tools To Improve Taxonomic Profiling – Vitor C. Piro – bioRxiv

Using null models to infer microbial co-occurrence networks – Nora Connor – PLOS ONE

Techniques

Characterization of microbial mixtures by mass spectrometry – Sandrin TR – Mass Spectrometry Reviews

Microbes in the news 

Cork scientists link gut bacteria to anxiety disorders

New tick bacteria in Australia being investigated as possible cause of Lyme disease-type illness

Optical nanofiber ‘hears’ bacteria swim, cancer cells move

Microbes on the market 

BiomX raises $24 million to boost bacteria based drugs

 

Ed’s non-microbiology picks

Breakthrough in delirium research ‘solves 2,500-year-old mystery’

Novel tissue-engineered islet transplant achieves insulin independence in type 1 diabetes – Bioengineering of an Intraabdominal Endocrine Pancreas -David A. Baidal – New England Journal of Medicine

High levels of exercise linked to nine years of less aging (at the cellular level)

Migratory birds bumped off schedule as climate change shifts spring

PrePrint – Using Social Network Analysis to Better Understand Compulsive Exercise Behavior among a Sample of Sorority Members –  Megan S. Patterson – Human Kinetics

Edible insects could play key role in cutting harmful emissions – EurkAlert!

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 27, 2017

An exploration of fish as an alternative to mice for models of host-microbe interactions, a review on what we can learn from Bacteroides about the gut micriobiome, a news story on successful phage therapy for a multi drug resistant infection.

Human oral microbiome

The human oral microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely-related individuals – Liam Shaw – bioRxiv

Human gut microbiome

* Review: An insider’s perspective: Bacteroides as a window into the microbiome – Aaron G Wexler – Nature Microbiology

Gut Microbiota: Small Molecules Modulate Host Cellular Functions – Jacob M. Luber – Current Biology

Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis – Tzipi Braun – Scientific Reports

Animal experiments

Supplemental feeding of a gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, alleviates spontaneous atopic dermatitis and modulates intestinal microbiota in NC/nga mice – Hiroko Kaikiri – International Journal of Food Sciences and Nutrition

Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation – Chris Flemming – Microbiome

Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction – Shiran Gerassy-Vainberg – Gut

Animal microbiome

Tick-Pathogen Interactions and Vector Competence: Identification of Molecular Drivers for Tick-Borne Diseases – José de la Fuente – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Review: Managing the plant microbiome for biocontrol fungi: examples from Hypocreales – Ryan M Kepler – Current Opinion in Microbiology

Occurrence of perchlorate in groundwater, paired farmland soil, lettuce, and rhizosphere soil from Chengdu, China – Yulu Tang – Environmental Science: Processes & Impact

Water and extremophile microbiome

The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions – Michael D Lee – The ISME Journal

Bringing methanotrophy in rivers out of the shadows – Felicity Shelley – Limnology and Oceanography

Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community – Andrea Di Cesare – Environmental Pollution

Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production – R Kanniah Goud – Bioresource Technology

Probiotics/prebiotics

Perspective: Next-generation probiotics: the spectrum from probiotics to live biotherapeutics – Paul W O’Toole – Nature Microbiology

Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ

Bioinformatics

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments – Arghya Mukherjee – Scientific Reports

Techniques

Faecal volatile organic compounds analysis using field asymmetric ion mobility spectrometry: non-invasive diagnostics in paediatric inflammatory bowel disease – Nora van Gaal – Journal of Breath Research

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

Synthetic and analytical strategies for the quantification of phenyl-γ-valerolactone conjugated metabolites in human urine – Nicoletta Brindani – Molecular Nutrition & Food Research

More microbes

Species ecological similarity modulates the importance of colonization history for adaptive radiation – Jiaqi Tan – International Journal of Organic Evolution

Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells – Yosuke Tashiro – Frontiers in Microbiology

Microbes in the news

Phage Therapy Saves Patient from Drug-Resistant Microbes – Genetic Engineering & Biotechnology News

Chronic fatigue syndrome linked to imbalanced microbiome – EurekAlert

Komodo Dragon Blood Could Become Tool in Fight Against Bacteria – Elizabeth Pratt – Healthline

Researchers move closer to preventing frost damage in vineyards by managing bacteria on the vines – Greg Northcutt – Western FarmPress

Underwater volcano eruptions allow new bacteria to take over seafloor – Lisa-Ann Lee – New Atlas

Microbes on the market

Taconic Biosciences Expands Microbiome Product and Service Platform – GlobeNewswire

Bacteria and art

This Art Exhibition Is Made From Bacteria, Live Insects And Human Sweat – Ryan F Mandelbaum – Gizmodo Australia

Art Made with CRISPR Aims to Raise Awareness of Antibiotic Resistance – Clara Rodríguez Fernández – Labiotech.eu

Amy’s non-microbiology picks

Microscopy: A larger palette for biological imaging – Charles H Camp Jr – Nature

April 18, 2017

Today’s digest hosts a number of rhizosphere-related publications as well as a good amount of interesting microbiome-host-health science.  Coming up next week is BioData World West 2017, a conference focused on Genomics/Precision Medicine/AI that I will be attending – I’ll keep an eye out for anything microbiome-related!

Events and jobs

2017 Metagenomics Workshop – Edwards Lab Event (Bioinformatics)

BioData World West 2017 – Precision Medicine, AI, Genomics Conference

General microbiome

Biological Determinants of Health: Genes, Microbes, and Metabolism Exemplars of Nursing Science – Erin P. Ferranti – Nursing Outlook

* Microbiotal-Host Interactions and Hypertension – Sarah Galla – Physiology

Multi-site human microbiome

The Landscape Ecology and Microbiota of the Human Nose, Mouth, and Throat – Diana M. Proctor – Cell Host & Microbe

Human respiratory microbiome

* The microbiome in respiratory medicine: current challenges and future perspectives – Rosa Faner – European Respiratory Journal

Human skin microbiome

Living in Peace: Host-Microbiota Mutualism in the Skin – Daniel J. Campbell – Cell Host & Microbe

Human gut microbiome

The Gut Microbiome: Connecting Spatial Organization to Function – Carolina Tropini – Cell Host & Microbe

Lactobacillus casei DG and its postbiotic reduce the inflammatory mucosal response: an ex-vivo organ culture model of post-infectious irritable bowel syndrome – Compare D – BMC Gastroenterology

Animal experiments

Age-Associated Microbial Dysbiosis Promotes Intestinal Permeability, Systemic Inflammation, and Macrophage Dysfunction – Netusha Thevaranjan – Cell Host & Microbe

Animal microbiome

PrePrint – Succession of embryonic and intestinal bacterial communities of Atlantic salmon – Jep Lokesh – bioRxiv

The Role of Rumen Microbiome on Feed Efficiency of Grazing Cattle [page 138] – Leluo Guan – 28th Annual Florida Ruminant Nutrition Symposium

Structure and dynamics of the gut bacterial microbiota of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) across their life stages – Carlos Iván Briones-Roblero – PLOS One

Plant, root, and soil microbiome

The role of soil chemistry and plant neighbourhoods in structuring fungal communities in three Panamanian rainforests – Tyler Schappe – Journal of Ecology

Host plant compatibility shapes the proteogenome of Frankia coriariae – Amir Ktari – Frontiers in Microbiology

Managing and manipulating the rhizosphere microbiome for plant health: A systems approach – Matthew D. Wallenstein – Rhizosphere

In vitro and In vivo biofilm formation by Azotobacter isolates and its relevance to rhizosphere colonization – Mohd. Musheer Altaf – Rhizosphere

Metabolism of pyrene through phthalic acid pathway by enriched bacterial consortium composed of Pseudomonas, Burkholderia, and Rhodococcus (PBR) – Sagar Vaidya – 3 Biotech

Effects of titanium dioxide nanoparticles on soil microbial communities and wheat biomass – Janine Moll – Soil Biology and Biochemistry

The effect of simulated warming on root dynamics and soil microbial community in an alpine meadow of the Qinghai-Tibet Plateau – Changting Wang – Applied Soil Ecology

Water and extremophile microbiome

Impacts of sea-level rise on sediment microbial community structure and function in two New England salt marshes, USA – Matt R. Simon – Journals of Soils and Sediments

A critical assessment of the microorganisms proposed to be important to enhanced biological phosphorus removal in full-scale wastewater treatment systems – Mikkel Stokholm-Bjerregaard – Frontiers in Microbiology

Applicability of cryoconite consortia of microorganisms and glacier-dwelling animals in astrobiological studies – Krzysztof Zawierucha – Contemporary Trends in Geoscience

Built environment

Review – Microbiological diagnosis of device-related biofilm infections – Yijuan Xu – APMIS

Patent Application – MONITORING AND MANAGING A FACILITY MICROBIOME – Dillon, Harrison – Free Patents Online

Microbes in space

Origins of Life on Mars: NASA’s Rovers Were Never Sterilized – Rhawn Gabriel Joseph – Cosmology.com

Phages and viruses

Mini Review Article – Phages in the Human Body – Ferran Navarro – Frontiers in Microbiology

Bioinformatics

* A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes – Wontack Han – Research in Computational Molecular Biology. RECOMB 2017.

Techniques

Effect of environmental variation on estimating the bacterial species richness – Jongjian Chen – Frontiers in Microbiology

Thesis – USE OF MOLECULAR METHODS IN BIOTHREAT PREPAREDNESS – Katja Koskela – National Defense University: Research Publications No. 13

Microbes in the news

Pets During Pregnancy Trigger Gut Bacteria Changes for Infants That May Cut Obesity Risk, Study Finds

Gut microbiome dysregulation implicated in OCD

Microbes on the market

Innovative Microbiome-based IBD Therapeutics to Be Developed Under New Partnership

Microbiome drug candidate prevents recurrence of C. difficile infection

Ed’s non-microbiology picks

Climate change causes glacial river in Yukon to change direction

Self-taught artificial intelligence beats doctors at predicting heart attacks

Stroke rates appear to be rising steadily in young adults

Costs of Selective Attention: When Children Notice What Adults Miss – Daniel J. Plebanek – APS

California Dryness and Recovery Challenge Multi-Century Odds

April 8, 2017

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