Category Archives: Events and jobs

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 12, 2017

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Highlighted articles today bring some interesting news about bacteria. in the first one study of Lebreton et al. shed light on the evolutionary history of pathogens, which evolved nearly indestructible properties and have become leading causes of modern antibiotic-resistant infections in hospitals. In the second highlighted article Schnettger et al. discover a natural mechanism by which our cells kill the bacterium responsible for tuberculosis (TB)  – without the use of antibiotics, meaning that even antibiotic-resistant
strains could be eliminated.

Events and jobs

Postdoctoral researcher – nitrogen-fixing bacteria and cereals

Postdoctoral Research Fellowship in Marine Phycology

General microbiome

Global Phylogenetic Analysis Of Escherichia coli And Plasmids Carrying The mcr-1 Gene Indicates Bacterial Diversity But Plasmid Restriction – Sebastien Matamoros – bioRxiv

Predictive compound accumulation rules yield a broad-spectrum antibiotic – Michelle F. Richter – Nature

Tracing the Enterococci from Paleozoic Origins to the Hospital – François Lebreton – Cell

The Threat of Antimicrobial Resistance on the Human Microbiome – Lauren Brinkac- Microbial Ecology

Evolutionary Biology Needs Wild Microbiomes – Sarah M. Hird – Frontiers in Microbiology

Pregnancy and early life

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome – Pia S. Pannaraj – JAMA Pediatr

Oral microbiome

The Antibacterial Effect of Additional Photodynamic Therapy in Failed Endodontically Treated Teeth: A Pilot Study – Mohammad Asnaashari – Journal of Lasers in Medical Science

Microbiota Analysis of Biofilms on Experimental Abutments Mimicking Dental Implants: An in Vivo Model – Berta Cortés-Acha – Journal of Periodontology

Human vaginal microbiome

Comparison of the vaginal environment in rhesus and cynomolgus macaques pre- and post-lactobacillus colonization – Gregory J. Daggett Jr – Journal of Medical Primatology

Human nearly-sterile sites (blood, organs, brain)

Active Trachoma Cases In The Solomon Islands Have Varied Polymicrobial Community Structures But Do Not Associate With Individual Non-Chlamydial Pathogens Of The Eye – Robert Butcher – bioRxiv

Human gut microbiome

Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases – Ashwin N. Ananthakrishnan – Cell Host & Microbiome

Current challenges in the treatment of severe Clostridium difficile infection: early treatment potential of fecal microbiota transplantation – Yvette H. van Beurden –
Therapeutic Advances in Gastroenterology

Review: Food additives, contaminants and other minor components: effects on human gut microbiota—a review – Paula Roca-Saavedra – Journal of Physiology and Biochemistry

Emulating Host-Microbiome Ecosystem of Human Gastrointestinal Tract in Vitro – Gun-Seok Park – Stem Cell Reviews and Reports

Animal experiments 

A Rab20-Dependent Membrane Trafficking Pathway Controls M. tuberculosis Replication by Regulating Phagosome Spaciousness and Integrity – Laura Schnettger – Cell host & Microbiome

Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium – Silvia Caballero – Cell Host & Microbe

Animal microbiome

Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats – James T. Price – PLoS ONE

A Meta-Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease – Huaishun Shen – Frontiers in Microbiology

Plant, root, and soil microbiome

Modifying And Reacting To The Environmental pH Drives Bacterial Interactions – Christoph Ratzke – bioRxiv

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity – Sigrid Dassen – Molecular Ecology

Analysis of the bacterial strains using Biolog plates in the contaminated soil from Riyadh community – Fahad Abdullah M. Al-Dhabaan – Saudi Journal of Biological Sciences

Biosurfactant-producing microorganism Pseudomonas sp. SB assists the phytoremediation of DDT-contaminated soil by two grass species – Beibei Wang – Chemosphere

Water and extremophile microbiome 

Molecular Diversity of Sea Spray Aerosol Particles: Impact of Ocean Biology on Particle Composition and Hygroscopicity – Richard E. Cochran – Chem, Cell Press

The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins – Ian P. G. Marshall – Environmental Microbiology Reports

Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1 – Yue Guan – Environmental Microbiology Reports

The Paradox Of Constant Oceanic Plastic Debris: Evidence For Evolved Microbial Biodegradation? – Ricard Sole – bioRxiv

Copper Pollution Increases the Resistance of Soil Archaeal Community to Changes in Water Regime – Jing LiYu-Rong Liu – Microbial Ecology

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA) – Jessica M. Morrison – PLoS ONE

Nitrotoga is selected over Nitrospira in newly assembled biofilm communities from a tap water source community at increased nitrite loading – Marta Kinnunen – Environmental Microbiology

Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond – Aurélien Saghaï – Environmental Micorbiology

Probiotics / prebiotics

Genotypic and phenotypic diversity of Lactobacillus rhamnosus clinical isolates, their comparison with strain GG and their recognition by complement system – Eija Nissilä – PLoS ONE

Bioinformatics

A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy – Xiang Gao – BMC Bioinformatics

gCoda: Conditional Dependence Network Inference for Compositional Data – Huaying Fang – Journal of Computational Biology

Effect of Lactobacillus rhamnosus HN001 and Bifidobacterium longum BB536 on the healthy gut microbiota composition at phyla and species level: A preliminary study – Marco Toscano – World Journal of Gastroenterology

Biotechnology

Review:Cyanobacterial metabolites as a source of sunscreens and moisturizers: a comparison with current synthetic compounds – Peyman Derikvand – European Journal of Phycology

Microbes in the news

Dramatic cooperation between two infectious bacteria revealed – Medicalxpress.com

Study finds bacteria in marine sponge produce toxic flame retardant-like compounds – Phys.org

Scientists Find Molecular ‘Key’ to Killing Hearty Bacteria – Extremetech.com

How our gut bacteria affect cancer risk and response to treatment – Theconversation.com

16S sequencing reveals differences between microbiomes in eyes, throat – Healio.com

Cosmetic Companies Now Develop Skin Care Products That Contain Live Bacteria To Treat Several Skin Problems – Sciencetimes.com

 

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

May 5, 2017

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A PLoS One paper, with Dr. Bik as one of the co-authors, to characterize human gut microbiome and compare certain taxa against healthy profiles, the relationship between diet, circadian rhythm and gut microbiome, and much more.

Events

Webinar: Interactions between the Mycobiome and Bacteriome: Impact on Health and Disease – Zymo Research

The Real Impact of Rodent Diet on Microbiome and Gut Health Research Webinar Q&A – Taconic

Jobs

PhD position in microbiology – Uppsala Universitet

Microbiology Technician – Pharmaceutical Industry – Runcorn

QC Microbiology/Environmental Control Associate – Yoh’s client – Phoenix

Human multi-site microbiome

Preprint: Microbial Metagenome Of Urinary Tract Infection – Ahmed Moustafa – bioRxiv

Human skin microbiome

Inhibition of fracture healing in the presence of contamination by Staphylococcus aureus: Effects of growth state and immune response – Krystle A. Blanchette et al. – Journal of Orthopaedic Research

Human gut microbiome

Conditional postnatal deletion of the neonatal murine hepatic circadian gene, Npas2, alters the gut microbiome following restricted feeding – Derek S. O’Neil et al. – American Journal of Obstetrics and Gynecology

Press: Study: Alterations to circadian clock change the body’s response to diet – Amy Wallace – UPI

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome – Daniel E. Almonacid and Laurens Kraal et al. (including our Elisabeth Bik) – PLoS One

Press: uBiome Publishes Peer-Reviewed Scientific Paper in PLOS ONE on First Version of Technology for Gut Health Screening Test – PRWeb

Commentary: The microbiota: an underestimated actor in radiation-induced lesions? – Harry Sokol and Timon Erik Adolph – Gut

Animal microbiome

Bacterial microbiota in small brown planthopper populations with different rice viruses – Shuo Li et al. – Journal of Basic Microbiology

Plant, root and soil microbiome

Small mammal activity alters plant community composition and microbial activity in an old-field ecosystem – Leigh C. Moorhead et al. – Ecosphere

Edaphic Conditions, Aboveground Carbon Stocks and Plant Diversity on Nickel Mine Tailings Dump Vegetated with Senegalia polyacantha (Willd.) Seigler & Ebinger – Edeth Mukaro et al. – Land Degradation & Development

Water and extremophile microbiome

Preprint: 290 Metagenome-assembled Genomes from the Mediterranean Sea: a resource for marine microbiology – Benjamin J Tully et al. – bioRxiv

Technology

Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli – Mojtaba Hasanpour and Akram Najafi – Journal of Microbiological Methods

New issue of the Journal of Microbiological Methods

Microbes in the news

Zika fight: Bacteria-laden mosquitoes unleashed in Florida to combat virus – Phil Keating – Fox News

Drought-quenching bacteria the future of farming? – Taylor Hartman – Daily Sun

Officials warn swimmers to avoid bacteria-laden parts of Lake Lanier – Ellen Eldridge – The Atlanta Journal-Constitution

Pathogenic bacteria train their defence in lakes and oceans – Phys.org

Cross-sector collaboration needed in fight against antimicrobial resistance – Sara Wyant – Agri-Pulse

Microbes on the market

Taconic Biosciences Expands Microbiome Portfolio – P&T Community

Careers

Microbiology Career Profiles – Market Specialist at Pacific Biosciences with Melissa Smith, PhD – ASM

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 19, 2017

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Exciting papers with locoregional effects of microbiota in a mouse model of colon carcinogenesis, maternal high fat diet detrimentally alterring epigenetic and gut microbiome pathways leading to fatty liver disease in mice.

Events and jobs

ASM Microbe 2017 : New Orleans

QC Microbiology Product Testing Associate – Experis : Irvine, CA
General microbiome

Review: Applying the design-build-test paradigm in microbiome engineering – Hoang Long Pham – Current Opinion in Biotechnology

Cohort Profile: African Collaborative Center for Microbiome and Genomics Research’s (ACCME) Human Papillomavirus (HPV) and Cervical Cancer Study – Sally N. Adebamowo – International Journal of Epidemiology

Review: Cultured microbes represent a substantial fraction of the human and mouse gut microbiota – Ilias Lagkouvardos – Gut Microbes

Human skin microbiome

A distinct cutaneous microbiota pofile in autoimmune bullous disease patients – Mor Miodovnika – Experimental Dermatology

Human gut microbiome

Review : A psychology of the human brain–gut–microbiome axis – Andrew P. Allen – Social and Personality Psychology Compass

Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs – Sean M P Bennet – Gut

Animal microbiome

Temporal changes in cutaneous bacterial communities of terrestrial- and aquatic- phase newts (Amphibia) – Joana Sabino-Pinto – Environmental Microbiology

The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa – Tomeu Viver – Environmental Microbiology

Studying the effect of administration route and treatment dose on the selection of enrofloxacin resistance in commensal Escherichia coli in broilers – Ilias Chantziaras -Journal of Antimicrobial Chemotherapy

The skin microbiome of the Common thresher shark (Alopias vulpinus) has low taxonomic and potential metabolic β-diversity – Michael P. Doane – Environmental Microbiology Reports

Animal experiments

Intestinal, extra-intestinal and systemic sequelae of Toxoplasma gondii induced acute ileitis in mice harboring a human gut microbiota – Eliane von Klitzing – PLOS ONE

Effects of the inclusion of a Bacillus direct-fed microbial on performance parameters, bone quality, recovered gut microflora, and intestinal morphology in broilers consuming a grower diet containing corn distillers dried grains with solubles – J. D. Latorre – Poultry Science

Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock – Shengyin Jiao – Journal of the Science of Food and Agriculture

*Locoregional effects of microbiota in a preclinical model of colon carcinogenesis – Sarah Tomkovich – Cancer Research

Selection of Cholesterol-Lowering Lactic Acid Bacteria and its Effects on Rats Fed with High-Cholesterol Diet – Yufang Liu – Current Microbiology

*Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations – Umesh D. Wankhade – PLOS ONE

Plant, root, and soil microbiome

Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion – Steven D Mamet- The ISME Journal

An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil – Masahito Hayatsu – The ISME Journal

Investigation of Arsenotrophic Microbiome in Arsenic-Affected Bangladesh Groundwater – Munawar Sultana – Groundwater

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses – Patricia Moya – Plos ONE

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii) – Qiang Li – Plos ONE

The ‘known’ genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils – Ian D. E. A. Lidbury – Microbiology Open

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations – M. S. Bray – Gebiology

Water and extremophile microbiome

Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats – Dimitry Y Sorokin – The ISME Journal

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system – Laura A Sauder – The ISME Journal

Minireview: Microbial ecology of mountain glacier ecosystems: Biodiversity, ecological connections, and implications of a warming climate – Scott Hotaling – Environmental Microbiology

Probiotics / prebiotics
Colonic gas homeostasis: Mechanisms of adaptation following HOST-G904 galactooligosaccharide use in humans – M. Mego – Neurogastroenterology and Motility

Techniques

Stochastically reduced communities—Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces – Jialan Cao – Engineering in Life Sciences

Protocol : Metagenomics and CAZyme Discovery – Benoit J. Kunath – Protein-Carbohydrate Interactions : Methods in Molecular Biology

The resident microflora of voided midstream urine of healthy controls: standard versus expanded urine culture protocols – L. Coorevits – European Journal of Clinical Microbiology & Infectious Diseases

Microbes in the news

Study finds amoeba ‘grazing,’ killing bacteria usually protected by film

How Bacteria-Laden Beetle Poop Is Killing American Squash and Melons

Glowing bacteria detect buried landmines

Science, publishing, and career

Saturday, Science Advocates Prepare for a Long March

Anitha’s non-microbiology picks

Research unlocks molecular key to animal evolution and disease

Cumulative culture can emerge from collective intelligence in animal groups – Takao Sasaki – Nature Communications

April 18, 2017

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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 14, 2017

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Quite a number of biofilms based reviews for today’s digest. Local adaptation in natural microbial communities. Bacterial community varies along the natural water balance gradient in the Tibetan Plateau.

Events and jobs

Senior Program Officer  – The Paul G. Allen Frontiers Group – Seattle, WA, United States

 

General microbiome

Culturomics: A New Kid on the Block of OMICS to Enable Personalized Medicine – ME Kambouris – Omics

Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution – T Giraud – Molecular Ecology

*Review: Central venous catheters and biofilms: where do we stand in 2017? – M Gominet – APMIS

 

Human oral microbiome

*Review: Dental biofilm infections – an update – T Larsen – APMIS

*Review: Microbiological diagnosis of device-related biofilm infections – Y Xu – APMIS

*Review: Biofilms in orthopedic infections: a review of laboratory methods – AC Dibartola – APMIS

 

Human vaginal microbiome

Vaginal lactic acid elicits an anti-inflammatory response from human cervicovaginal epithelial cells and inhibits production of pro-inflammatory mediators associated with HIV acquisition – AC Hearps – Mucosal Immunology

*Review: Chronic urinary tract infections in patients with spinal cord lesions – biofilm infection with need for long-term antibiotic treatment – N Tofte – APMIS

 

Human gut microbiome

Curcuminoid Demethylation as an Alternative Metabolism by Human Intestinal Microbiota – S Burapan – Journal of Agricultural and Food Chemistry

Inflammasomes and intestinal inflammation – N Zmora – Mucosal Immunology

Gut Microbial Diversity in Antibiotic-Naive Children After Systemic Antibiotic Exposure: A Randomized Controlled Trial – T Doan – Clinical Infectious Diseases

 

Animal microbiome

Fish oil, lard and soybean oil differentially shape gut microbiota of middle-aged rats – He Li – Scientific Reports

Co-diversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence – L Kropáčková – Molecular Ecology

 

Plant, root and soil microbiome

Responses of denitrifying bacterial communities to short-term waterlogging of soils – Y Wang – Scientific Reports

Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau – Y Li – Scientific Reports

Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient – KG Peay – FEMS Microbiology Ecology

Continuous production of indole-3-acetic acid by immobilized cells of Arthrobacter agilis – M Ozdal – 3 Biotech

*Review: Agriculturally important microbial biofilms: Present status and future prospects – K Velmourougane – Journal of Basic Microbiology

 

Water and extremophile

Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana – Y Liang – Environmental Science and Pollution Research International

Spatial variation in bacterial community in natural wetland-river-sea ecosystems – H Zhang – Journal of Basic Microbiology

Bioremediation Management Reduces Mass Discharge at a Chlorinated DNAPL Site – BR Baldwin – Groundwater Monitoring & Remediation

 

Techniques

Enhancing Multiplex Genome Editing by Natural Transformation (MuGENT) via inactivation of ssDNA exonucleases – TN Dalia – bioRxiv

An Efficient Moments-Based Inference Method for Within-Host Bacterial Infection Dynamics – D Price – bioRxiv

 

More microbes

Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle – S Mandal De – BMC Microbiology

Microbiome yarns: microbiomology of winter rosy face – K Timmis – Microbial Biotechnology

*Review: In vitro studies evaluating the effects of biofilms on wound-healing cells: a review – KR Kirker – APMIS

Vector competence and innate immune responses to dengue virus infection in selected laboratory and field-collected Stegomyia aegypti (= Aedes aegypti) – IM Serrato – Medical and Veterinary Entomology

*Review: Antibiotic treatment of biofilm infections – O Ciofu – APMIS

Microenvironmental characteristics and physiology of biofilms in chronic infections of CF patients are strongly affected by the host immune response – PØ. Jensen – APMIS

 

Microbes in news

To see the unseen: ‘Microbiomes’ show explores the common ground between arts, science – M McINALLY – Gazette-Times

Unprotected sex may disrupt the microbiome in vagina – J Hamzelou – New Scientist

Sol-gel-based stainless steel surface reduces fouling and biofilm formation during milk pasteurization – J Cornall- Dairy Reporter

Gut Microbes Contribute to Age-Associated Inflammation in Mice – A Olena – The Scientist

Microbiome Plus+ Gastrointestinal: New Probiotic Supplement Proven to Increase Vitamin D Levels While Lowering Cholesterol – Military News – Miltech

OPINION: How probiotics research is taking us to the next level of understanding – M Cunningham – Food Navigator

New synthetic peptide promotes wound healing – T Sandle – Digital Journal

Air Pollution Might Make Dangerous Bacteria Harder to Kill – V Greenwood – The Atlantic

Researchers studying how to disrupt bacteria to better treat infections – Phys.org

Bacteria with a bias – K Zehr – UNM HSC Newsbeat

Glowing bacteria could help in landmine cleanup efforts – D Quick – New Atlas

Trump budget plan could sink Shore beaches bacteria reports – R Zimmer – Asbury Park Press

How genetically-altered E.coli strain can kill dangerous bone-eating superbug Pseudomonas aeruginosa – B Crouch – The Advertiser

Study on lactic acid bacteria from kimchi sheds light on treatment of atopic dermatitis – The Korea Herald

This strain of probiotic bacteria treats and protects against anxiety, stress and inflammation – St. Joseph’s Healthcare

 

April 12, 2017

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A pretty broad Digest today, with a promising phylogenetic marker for fungal community studies, a new issue of the Journal of Microbiological Methods, and several news pieces, including one about brain stimulating for weight loss.

Jobs

Microbiology Technician – Lonza America Inc

BMS Microbiology – South West England

General microbiology

*A new promising phylogenetic marker to study the diversity of fungal communities: the GLYCOSIDE HYDROLASE 63 gene – L. Pérez-Izquierdo – Molecular Ecology Resources

pH-Controlled Cerium Oxide Nanoparticle Inhibition of Both Gram-Positive and Gram-Negative Bacteria Growth – Ece Alpaslan – Scientific Reports

Human oral microbiome

The probiotics in dentistry: a narrative review – A.M. Pujia – European Review for Medical and Pharmacological Sciences

Human ear microbiome

Microbiomes of the normal middle ear and ears with chronic otitis media – Shujiro B. Minami – Laryngoscope

Human gut microbiome

PrePrint: Household triclosan and triclocarban exposure impacts the adult intestinal microbiome but not the infant intestinal microbiome – Jessica V. Ribado – bioRxiv

Corrigendum: Antibiotic treatment at delivery shapes the initial oral microbiome in neonates – Luisa F. Gomez-Arango – Scientific Reports

Seven versus 10 days antibiotic therapy for culture-proven neonatal sepsis: A randomised controlled trial – Smriti Rohatgi – Journal of Paediatrics and Child Health

Animal experiments

Metabolic adaptation to the aqueous leaf extract of Moringa oleifera Lam.-supplemented diet is related to the modulation of gut microbiota in mice – Xiaoyu Gao – Applied Microbiology and Biotechnology

Bioactive Molecule from Streptomyces sp Mitigates MDR Klebsiella pneumoniae in Zebrafish Infection Model – Lalitha Cheepurupalli – Frontiers in Microbiology

Animal microbiome

Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing – Mao Li – Scientific Reports

Plant, root and soil microbiome

Biological Control of Bacterial Fruit Blotch of Watermelon Pathogen (Acidovorax citrulli) with Rhizosphere Associated Bacteria – Mahesh Adhikari – The Plant Pathology Journal

Book Chapter: Ecological Restoration Techniques for Management of Degraded, Mined-Out Areas and the Role Played by Rhizospheric Microbial Communities – Prashant Pant & Pratibha Pant – Green Technologies and Environmental Sustainability

Abstract: Consistently inconsistent drivers of patterns of microbial diversity and abundance at macroecological scales – Hendershot JN – Ecology

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere – Sadaf Kalam – Journal of Basic Microbiology

Water and extremophile microbiome

Abstract: Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon – P. Behera – Science of the Total Environment

PDF: The Effects of Soil Environmental Factors on the Colonization of Marine Biocontrol Bacteria – Zenghai Bao – Journal of Residuals Science & Technology

Book chapter: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad & Juan M. Gonzalez – Microbial Applications Vol.1

Effects of short-term warming and altered precipitation on soil microbial communities in alpine grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance – Weixiong Lin – Ecotoxicology and Environmental Safety

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities – Heikki Mykrä – Oikos

Microbes in space

Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions – Giorgio Casaburi – Scientific Reports

Phages and viruses

iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus – Songbai Yang – Scientific Reports

Technology

Release of a new issue of the Journal of Microbiological Methods, with various technical articles of potential interest.

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models – Chao Ye – Scientific Reports

Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding – Panu Somervuo – Methods in Ecology and Evolution

Microbes in the news

DIRTY PINTS One in three pints served in pubs use ‘bad’ bacteria-filled beer because landlords aren’t cleaning the pumps properly – Sara Kamouni – The Sun

Melioidosis: More cases of potentially fatal bacterium from NT dirt emerge – Eleni Rousos – ABC News

*Magnetic brain stimulation causes weight loss – Tim Sandle – Digital Journal

5 Ways to Ruin Wine Before It’s Even Bottled – Laura Burgess – Vine Pair

A public health failure – Otago Daily Times

Study to develop faster detection of antibiotic resistance – Scoop

Microbes on the market

Superbugs receive a dual drug attack – Kate Dearling – The Badger Online

Breast Milk Helps In The Growth Of Microbes Beneficial To Human Colon, Best For Babies Too – Jezreel Smith – The Science Times

April 11, 2017

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In today’s Microbiome Digest the first interesting study comes not from bacteria but from virus domain. Examining the genomes within a sample from a wastewater treatment plant in Austria, Schulz et al. assembled a previously undiscovered giant virus genome with more genes encoding components of the protein translation machinery than in other giant viruses. The second highlighted  study introduces new oleaginous microalga as a new potential source of compounds for biotechnological applications.

Events and jobs

QC Microbiology Analyst – Dublin, Ireland

Assistant Lecturer in Microbiology – Sligo, Ireland

General microbiome

The genetics of human longevity: an intricacy of genes, environment, culture and microbiome – Serena Dato – Mechanisms of Ageing and Development

Pregnancy and early life

Correlation between early-life regulation of the immune system by microbiota and allergy development – Thomas Gensollen – Journal of Allergy and Clinical Immunology

Microbial Community Assembly And Metabolite Profile Of The Gut Microbiome In Extremely Low Birthweight Infants – Stephen Wandro – bioRxiv

Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum – Chihaya Yamada – Cell Chemical Biology

A Comparative Study of Oral Microbiota in Infants with Complete Cleft Lip and Palate or Cleft Soft Palate – Agnieszka Machorowska-Pieniążek – BioMed Research International

Effect of probiotics on digestibility and immunity in infants: A study protocol for a randomized controlled trial – Lingli Xiao – Medicine

Human respiratory microbiome

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

Oral microbiome

Measuring nitrate reductase activity from human and rodent tongues – Khandaker Ahtesham Ahmed – Nitric Oxide

Streptococcal adhesin SspA/B analogue peptide inhibits adherence and impacts biofilm formation of Streptococcus mutans – Tatsuro Ito – PLOSOne

Characterization of growth inhibition of oral bacteria by sophorolipid using a microplate-format assay – Daniel K.Y. Solaiman – Journal of Microbiological Methods

Salivary microbiome of an urban Indian cohort and patterns linked to subclinical inflammation  – Aneesha Acharya – Oral Diseases

Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment – M.M. Nascimento – Journal of Dental Research

Human skin microbiome

Bacterial communities on facial skin of teenage and elderly Thai females – Naraporn Somboonna – Archives of Microbiology

Skin microbiome and mast cells – Satomi Igawa – Translational Research

Human vaginal microbiome
Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods

‘Anaerococcus mediterraneensis’ sp. nov., a new species isolated from human female genital tract – K. Diop – New Microbes and New Infections

Human gut microbiome

Functional relevance of microbiome signatures: The correlation era requires tools for consolidation – Ludovica F. Buttó – Journal of Allergy and Clinical Immunology

Physiochemical Tuning of Potent Escherichia coli Anti-Adhesives by Microencapsulation and Methylene Homologation – Dimitri Alvarez Dorta – ChemMedChem

Gut microbiota functions: metabolism of nutrients and other food components –  Ian Rowland – European Journal of Nutrition

Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS–based metabolomics approach – Eikan Mishima – Kidney International

Animal experiments

Starch-enriched diet modulates the glucidic profile in the rat colonic mucosa – Maria Gabriella Gabrielli – European Journal of Nutrition

The influence of diet on the grass carp intestinal microbiota and bile acids – Jing Zhang – Aquaculture Research

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves – D.E. Gomez – Journal of Veterinary Internal Medicine

Gut Microbiota Modulation Attenuated the Hypolipidemic Effect of Simvastatin in High-Fat/Cholesterol-Diet Fed Mice – Xuyun He – Journal of Proteome Research

 

Animal microbiome

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut – Clayton M. Small – Genome Biology and Evolution

The structured diversity of specialized gut symbionts of the New World army ants – Piotr Łukasik – Molecular Ecology

Microbial composition of spiny ants (Hymenoptera: Formicidae: Polyrhachis) across their geographic range – Manuela Oliveira Ramalho – BMC Evolutionary Biology

Plant, root, and soil microbiome

Isolation, identification, and environmental adaptability of heavy-metal-resistant bacteria from ramie rhizosphere soil around mine refinery – Jie Jiang – Biotech

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities – Stephanie D. Jurburg – Scientific Reports

Microbial community response to hydration-desiccation cycles in desert soil – Adam Šťovíček – Scientific Reports

Water and extremophile microbiome

Development of an economical, autonomous pHstat system for culturing phytoplankton under steady state or dynamic conditions – Rachel L. Golda – Journal of Microbiological Methods

Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods – Sarita Pudasaini – Frontiers in Microbiology

Subduction zone forearc serpentinites as incubators for deep microbial life – Oliver Plümper – PNAS

Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago) – G. Bortoluzzi – Geobiology

Microbial biotechnology

Characterization of a Chlorophyta microalga isolated from a microbial mat in Salar de Atacama (northern Chile) as a potential source of compounds for biotechnological applications – Gladys Hayashida – Phycological Research

Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae – Vineeta Rai – Scientific Reports

Food microbiology

Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland – Agnieszka Kalwasińska – Antonie van Leeuwenhoek

Probiotics / prebiotics

Genome Sequences of Potential Probiotic Lactobacillus rhamnosus Isolates from Human Infants – Jason W. Arnold – Genome Announcements

Phages and viruses

Review: Phage injection establishes CRISPR immunity – Shimona Starling – Nature Reviews Microbiology

Giant viruses with an expanded complement of translation system components – Frederik Schulz – Science

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

Techniques

Identification of microorganisms grown on chromogenic media by MALDI-TOF MS – Petra Lüthje – Journal of Microbiological Methods

The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli – Sylvia Omulo – Journal of Microbiological Methods

Chapter in the book: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad – Microbial Applications Vol.1

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling – Stefan A. Boers – Scientific Reports
Microbes in the news 

Bacteria to the Future – Mizzou News (University of Missouri)