Category Archives: Metagenomics & Bioinformatics

17, July 2017

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In today’s digest, we learn more about how cloud-based computing is making it easier to analyses big datasets, and stochastic bottlenecks control bacterial colonization in animal host.

General Microbiome and Microbiology

New perspectives on dandruff and seborrheic dermatitis: lessons we learned from bacterial and fungal skin microbiota.

Paulino LC. European journal of dermatology

Harnessing microbiome‐based biotechnologies for sustainable mitigation of nitrous oxide emissions

Hu HW.Microbial Biotechnology

Human gut microbiome

Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer. Yoon H. Journal of Cancer Prevention

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Xiong W. Microbiome

Assessing the impact of protein extraction methods for human gut metaproteomics

Zhang  X.Journal of Proteomics

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

Stewart CJ. Microbiome

Animal and insect microbiome

Host–Microbe Interactions: Winning the Colonization Lottery

Lazzaro BP and GM Fox. Current Biology

Strategies for managing rival bacterial communities: lessons from burying beetles.

Kilner RM. Journal of Animal Ecology

Changes in the Gut Microbial Communities Following Addition of Walnuts to the Diet. Byerley, LO. Journal of Nutritional Biochemistry

Microbiome modelling

The Microbiome and Big Data

Navas-Molina JA. Current Opinion in Systems Biology

Plant, soil, and air microbiome

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US.

Kaleita AL.PloS one

Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata

Zhao M. Applied Soil Ecology

Changes in microbial community composition following phytostabilization of an extremely acidic Cu mine tailings

Yang T. Soil Biology and Biochemistry

Effects of between‐site variation in soil microbial communities and plant‐soil feedbacks on the productivity and composition of plant communities.   Bauer JT.Journal of Applied Ecology

Response of soil microbial communities to elevated antimony and arsenic contamination indicates the relationship between the innate microbiota and contaminant fractions. Sun W. Environmental Science and Technology

Marine and inland waters

The contribution of microbial biotechnology to mitigating coral reef degradation Damjanovic. Microbial Biotechnology

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby BM. The ISME Journal

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

He T.  mBio

Built Microbiome

Microbial communities on painted wet and dry external surfaces of a historic fortress in Niterói, Brazil. Ogawa A. Journal of International Biodeterioration & Biodegradation

Preprint

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.Gerth M.PeerJ

July 7, 2017

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Human Microbiome

Review: Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis – Liu et al. – Digestive and Liver Disease

Non-antibiotic Isotretinoin treatment differentially controls Propionibacterium acnes on skin of acne patients. – Ryan-Kewley et al. – Frontiers in Microbiology

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy – Namasivayam et al. – Microbiome (BMC)

Research Highlights: Obesity: Gut microbiome and serum metabolome changes – Claire Greenhill – Nature Reviews Endocrinology

Research Highlights:  Gut microbiota: Link between the gut and adipose tissues – Alan Morris – Nature Reviews Endocrinology

Review: The gut microbiome and liver cancer: mechanisms and clinical translation – Yu & Schwabe – Nature Reviews Gastroenterology and Hepatology

 

Pathogens

Reactive Oxygen Species-Dependent Essential Genes in Salmonella Typhimurium – Karash and Min Kwon – BioRxiv

Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes – Wang et al – Scientific Reports (Nature)

Effects of different substrates/growth media on microbial community of saliva-derived biofilm – Li et al – FEMS Microbiology letters

 

Methods (including bioinformatics)

Selective imaging of Gram-negative and Gram-positive microbiotas in the mouse gut – Wang et al. – Biochemistry (ACS)

Methodology: VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data – Ren et al. – Microbiome (BMC)

Methodology: A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform – de Muinck et al. – Microbiome (BMC)

Completing bacterial genome assemblies with multiplex MinION sequencing – Wick et al. – BioRxiv

Axe: rapid, competitive sequence read demultiplexing using a trie – Murray & Borevitz – BioRxiv

 

Water microbiome

Unraveling the microbial interactions and metabolic potentials in pre- and post-treated sludge from a wastewater treatment plant using metagenomic studies – Sidhu et al. – Frontiers in Microbiology

Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River – Henson et al. – BioRxiv

 

Extremophiles

Oxidative weathering and microbial diversity of an inactive seafloor hydrothermal sulfide chimney – Li et al. – Frontiers in Microbiology

Hidden biofilms in a far northern lake and implications for the changing Arctic – Mohit et al. – npj Biofilms and Microbiomes

 

Probiotics – Fermented Food

Amplicon sequencing of the slpH locus permits culture-independent strain typing of Lactobacillus helveticus in dairy products – Moser et al. – Frontiers in Microbiology

Probiotic Enterococcus mundtii Isolate Protects the Model Insect Tribolium castaneum against Bacillus thuringiensis – Grau et al. – Frontiers in Microbiology

 

Animal Microbiome

Regulation of gut luminal serotonin by commensal microbiota in mice –  Hata et al. – PLoS ONE

 

News

News: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh via Scientific American Mind (Nature)

News: Mind over Meal: Does Weight-Loss Surgery Rewire Gut-Brain Connections? – Bret Stetka via Scientific American Mind (Nature)

 

Fellowships

Post-Doctoral Research Fellow, Microbiome and Vaccine Induced Immunity – Seattle, WA, United States

Postdoctoral Fellow (Listeria monocytogenes research) – Dunedin, New Zealand

 

Other

The earth is flat (p > 0.05): significance thresholds and the crisis of unreplicable research – Amrhein et al. – PeerJ

 

July 6, 2017

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The microbiota of spotted hyenas, a review of potential interactions between olfactory sensation and the microbiome-gut-brain axis, phylogenetic analysis of host-microbe symbioses to examine the evolution of dependence over time.

General microbiome

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia – Sami Ben Said – Frontiers in Microbiology

The evolution of host-symbiont dependence – Roberta M Fisher – Nature Communications

Review: The microbiota revolution: Excitement and caution – Maria Rescigno – European Journal of Immunology

Review: The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure? – Souhaila Al Khodor – Frontiers in Pediatrics

Human oral microbiome

Suppression of αvβ6 Integrin Expression by Polymicrobial Oral Biofilms in Gingival Epithelial Cells – Jiarui Bi – Scientific Reports

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus – Kai Bao – Scientific Reports

Human vaginal microbiome

Quantifying the human vaginal community state types (CSTs) with the species specificity index – Zhanshan Ma – PeerJ

Animal experiments

Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups – Erica E Alexeev – PLOS ONE

Review: Disruptive physiology: olfaction and the microbiome-gut-brain axis – John Bienenstock – Biological Reviews Cambridge Philosophical Society

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice – Hui Dong – BMC Microbiology

Animal microbiome

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition – Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Perspective: The deep, hot biosphere: Twenty-five years of retrospection – Daniel R Colman – PNAS

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – Gabriel L Lozano – Genome Announcements

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland – Johanna Birgander – Global Change Biology

Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework – Briana K Whitaker – Ecology Letters

Water and extremophile microbiome

Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis – Thomas W Evans – Organic Geochemistry

FurukawaMarine microbes as a valuable resource for brand new industrial biocatalysts – Azadeh Beygmoradi – Biocatalysts and Agricultural Biotechnology

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens) – M Fujimoto – Microbial Ecology

Probiotics/prebiotics

Effects of the probiotic Bifidobacterium animalis subsp. lactis on the non-surgical treatment of periodontitis. A histomorphometric, microtomographic and immunohistochemical study in rats – Milla S T Ricoldi – PLOS ONE

Phages and viruses

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics – Mohammad Moniruzzaman – Nature Communications

Occurrence of Bacillus thuringensis Bacteriophages in the Egyptian Arid Soil – Amel S M Abo-Senna – International Journal of Virology and Molecular Biology

Bioinformatics

A conceptual framework for quality assessment and management of biodiversity data – Allan Koch Veiga – PLOS ONE

Techniques

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures – Joost Willemse – bioRxiv

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem – Arisa Tsuboi – bioRxiv

More microbes

Review: Metabolic engineering pathways for rare sugars biosynthesis, physiological functionalities, and applications – A review – Muhammad Bilal – Critical Reviews in Food Science and Nutrition

Microbes in the news

Microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman – Medical Xpress

What Cheese Can Tell Us About Antibiotic Resistance – Jason Tetro – Huffington Post Canada

Cases of recurrent Clostridium difficile infection are soaring – Medical Xpress

Helium ions reveal how viruses attack bacteria – ScienceDaily

July 5, 2017

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General microbiome

Letter to the editor: Introducing the sporobiota and sporobiome – George Tetz – Gut Pathogens

Human oral microbiome

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Hai-Yue Liu – Frontiers in Microbiology

Human respiratory microbiome

Review: Respiratory microbiota and lower respiratory tract disease – Miguel Lanaspa – Expert Review of Anti-infective Therapy

Human gut microbiome

Review: Feeding the microbiota: transducer of nutrient signals for the host – Fergus Shanahan – Gut

Animal microbiome

Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs – Brian D Piccolo – The Journal of Nutrition

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major) – Lucie Kropáčková – Plos One

Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin – Ana V. Longo – Molecular Ecology

Early-Life Diet Affects Host Microbiota and Later-Life Defenses Against Parasites in Frogs – Sarah A. Knutie – Integrative & Comparitive Biology

Animal experiments

Relative variations of gut microbiota in disordered cholesterol metabolism caused by high-cholesterol diet and host genetics – Tao Bo – Microbiology Open

Plant, root, and soil microbiome

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities – Kelly Gravuer – Frontiers in Microbiology

Long-term rock phosphate fertilization impacts the microbial communities of maize rhizosphere – Ubiana C. Silva – Frontiers in Microbiology

Global change and the soil microbiome: A human-health perspective – Raúl Ochoa-Hueso – Frontiers in Ecology and Evolution

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms – Adam Št’ovíček – Frontiers in Microbiology

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand – Jocelyn C. Griffith – Plos One

Water and extremophile microbiome

Bacterial diversity and population shifts driven by spotlight wastewater micropollutants in low-temperature highly nitrifying activated sludge – Antonina Kruglova – JScience of The Total Environment

Probiotics / prebiotics

The potential synergistic behaviour of inter- and intra-genus probiotic combinations in the pattern and rate of short chain fatty acids formation during fibre fermentation – Warnakulasuriya M. A. D. B. Fernando – International Journal of Food Sciences and Nutrition

Review: Structural features underlying prebiotic activity of conventional and potential prebiotic oligosaccharides in food and health – Subin R. C. K. Rajendran – Journal of Food Biochemistry

Phages and viruses

Case control comparison of enteric viromes in captive rhesus macaques with acute or idiopathic chronic diarrhea – Beatrix Kapusinszky – Journal of Virology

A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections – Samuele Bovo – Plos One

Bioinformatics

Does colorectal cancer significantly influence the assembly of gut microbial communities? – Lin Dai – PeerJ

Review: Using metagenomics to investigate human and environmental resistomes – Johan Bengtsson-Palme – Journal of Antimicrobial Chemotherapy

RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards – Stephen Salerno Jr – Plos One

Predicting the ecological quality status of marine environments from eDNA metabarcoding data using supervised machine learning – Tristan Cordier – Environmental Science and Technology

Anitha’s non-microbiology picks

AI is changing how we do science. Get a glimpse

Scientists explain ancient Rome’s long-lasting concrete

June 23, 2017

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Human Microbiome

Genome reconstruction and characterisation of extensively drug-resistant bacterial pathogens through direct metagenomic sequencing of human faeces – Mu et al. – BioRxiv

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Liu et al. – Frontiers in Microbiology

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

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis – Tett et al. – npj Biofilms and Microbiomes

Rosacea and its association with enteral microbiota in Korean females – Nam et al. – Experimental Dermatology

Review: The role of microbiota, and probiotics and prebiotics in skin health – Maguire & Maguire – Archives of Dermatological Research

Human age and skin physiology shape diversity and abundance of Archaea on skin – Moissl-Eichinger et al. – Scientific Reports

Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas – Banerjee et al. – Scientific Reports

 

Animal Microbiome

Gut Dysbiosis and Adaptive Immune Response in Diet-induced Obesity vs. Systemic Inflammation – Pindjakova et al. – Frontiers in Microbiology

Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys –  Wilkinson et al. – Frontiers in Microbiology

Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasis – Shen et al. – Scientific Reports

Fatty acid composition and phospholipid types used in infant formulas modifies the establishment of human gut bacteria in germ-free mice –  Guldhammer Nejrup et al. – Scientific Reports

Microbiota-derived butyrate suppresses group 3 innate lymphoid cells in terminal ileal Peyer’s patches – Kim et al. – Scientific Reports

Early-life gut microbial colonization shapes Th1/Th2 balance in asthma model in BALB/c mice – Qin et al. – BMC Microbiology

The development of lower respiratory tract microbiome in mice – Singh et al. – Microbiome (BMC)

 

Pathogen research

Genetic indicators of drug resistance in the highly repetitive genome of Trichomonas vaginalis – Bradic et al. – Genome Biology and Evolution

Metabolic and fitness determinants for in vitro growth and intestinal colonization of the bacterial pathogen Campylobacter jejuni – Gao et al. – PLoS Biology

Review: Periodontal diseases – Kinane et al. – Nature Reviews Disease Primer

 

Soil and Water Microbiome

Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge – McIlroy et al. – Frontiers in Microbiology

Nitrogen enrichment impacts on boreal litter decomposition are driven by changes in soil microbiota rather than litter quality – Maaroufi et al. – Scientific Reports

 

Bioinformatics

CD-HIT-OTU-MiSeq, an Improved Approach for Clustering and Analyzing Paired End MiSeq 16S rRNA Sequences – Li et al. – BioRxiv

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments – Yim​ & Cushman – PeerJ

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters – Cheng et al. – PeerJ Preprints

 

Evolution

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells – Nasir et al. – Frontiers in Microbiology

Pan-genome and phylogeny of Bacillus cereus sensu lato – Bazinet – BioRxiv

TreeTime: maximum likelihood phylodynamic analysis – Sagulenko et al. – BioRxiv

 

Other

Review: Fungal and Bacterial Pigments: Secondary Metabolites with Wide Applications –  Morris et al. – Frontiers in Microbiology

A Highly Efficient CRISPR-Cas9-Mediated Large Genomic Deletion in Bacillus subtilis – So et al. – Frontiers in Microbiology

June 22, 2017

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Effects of weight loss treatment on gut microbiota and serum metabolites, mouse gut microbiota can alter visceral sensitivity, a review discussing the microbiota’s ability to shape the maternal immune system.

Pregnancy and early life

Review: The unique immunological and microbial aspects of pregnancy – Gil Mor – Nature Reviews Immunology

Human oral microbiome

Review: Microbiome and Microbial Biofilm Profiles of Peri-Implantitis: A Systematic Review – Gloria Inés Lafaurie – Journal of Periodontology

Human gut microbiome

Bifidobacterium-Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome – S Mizuno – Digestion

Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests – Francesca Borgo – PLOS ONE

Animal experiments

Fructo-oligosaccharides and intestinal barrier function in a methionine–choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS ONE

Microbiota regulates visceral pain in the mouse – Pauline Luczynski – eLife

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle – Milton Thomas – bioRxiv

Animal microbiome

Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut – Angela Kruse – PLOS ONE

Plant, root, and soil microbiome

Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere – Qing-Lin Chen – Environmental Science & Technology

Water and extremophile microbiome

Synergistic hydrolysis of xylan using novel xylanases, β-xylosidases, and an α-l-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2 – Di Huang – Applied Microbiology and Biotechnology

Longitudinal variation of microbial communitiesin benthic biofilms and association with hydrological and physicochemical conditions in glacier-fed streams – Ze Ren – Freshwater Science

Control of Sulfide Production in High Salinity Bakken Shale Oil Reservoirs by Halophilic Bacteria Reducing Nitrate to Nitrite – Biwin A An – Frontiers in Microbiology

Phages and viruses

Viral and Bacterial Communities of Colorectal Cancer – Geoffrey D Hannigan – bioRxiv

Plasmids, Viruses, And Other Circular Elements In Rat Gut – Tue Sparholt Jørgensen – bioRxiv

Bioinformatics

The metagenomic data life-cycle: standards and best practices – Petra ten Hoopen – GigaScience

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies – Ludovic Mallet – Bioinformatics

Metabolomics

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention – Ruixin Liu – Nature Medicine

Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease – Robert A Quinn – American Journal of Respiratory and Critical Care Medicine

Coupling targeted and untargeted mass spectrometry for metabolome-microbiome-wide association studies of human fecal samples – Alexey V Melnik – Analytical Chemistry

Techniques

Incorporating comparative genomics into the Design-Test-Learn cycle of microbial strain engineering – Maria Sardi – FEMS Yeast Research

Different amplicon targets for sequencing-based studies of fungal diversity – Francesca De Filippis – Applied and Environmental Microbiology

Microbes in the news

Modified viruses deliver death to antibiotic-resistant bacteria – Sara Reardon – Nature

Microbes on the market

EnteroBiotix raises £500k in first round of equity funding – Philip Gates – Insider.co.uk

Microbiotica To Present At Microbiome Drug Development Summit – BioSpace

Bacteria art

MIT Researchers Use Light-Illuminated Bacteria to Make ‘Living’ Pictures – Kristin Fawcett – Mental Floss

The world’s art is under attack—by microbes – Kate Baggaley – Popular Science

Science, publishing, and career

Editorial: Don’t let Europe’s open-science dream drift – Nature

June 21, 201

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Today’s Microbiome Digest has quite a few articles from water environment. Both articles I would like to highlight are with cyanobacteria as stars. The first one from Anne D. Jungblut reports on Antarctic cynobacteria diversity, while the second one reveals the new freshwater cyanobacterial genome. One more thing to highlight come from news. Exxon Mobil Corps and Sintetic Genomics Inc have announced a new breakthrough with genetically modified algae which was able to convert 40% of CO2 to lipids, up from the previous 15%. Algae are still far away from being able to run the process at commercial scale and replace fossil fuels, but we love algae! Enjoy this summer reading.

Events and jobs

Microbiome Research Scientist (BS or MS or PhD) – St. John of God Foundation for Research and Teaching, Barcelona, Spain

Quality Associate Specialist – Merck, Durham, NC, US

Microbiology Manager OR Microbiology Laboratory Manager Opening, Madison, WI, US
General microbiome

A null model for microbial diversification – Timothy J. Straub – PNAS

Pregnancy and early life

Association between breast milk bacterial communities and establishment and development of the infant gut microbiome – JAMA Pediatrics
Human skin microbiome

Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by competitors – Adam J. SanMiguel – Antimicrobial Agents and Chemotherapy
Human gut microbiome

Liver transplant modulates gut microbial dysbiosis and cognitive function in cirrhosis – Jasmohan S. Bajaj – Liver Transplatation

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans – Alan Cartmell – PNAS

Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – Kate Lawrence – PLOS
Animal microbiome 

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – The ISME Journal
Plant, root, and soil microbiome

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions – Di Wang – The ISME Journal

Novel antibiotic resistance determinants from agricultural soil exposed to antibiotics widely used in human medicine and animal farming – Calvin Ho-Fung Lau – Applied and Environmental Microbiology
Water and extremophile microbiome 

Animal-like prostaglandins in marine microalgae – Valeria Di Dato – The ISME Journal

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents – Dimitri V Meier – The ISME Journal

Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway – Ian Lidbury – The ISME Journal

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments – Anders Lanzén – PLOS

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters – David M Needham – The ISME Journal

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics – Lucas Moitinho-Silva – The ISME Journal

Spontaneous mutations of a model heterotrophic marine bacterium – Ying Sun – The ISME Journal

Plastid thylakoid architecture optimizes photosynthesis in diatoms – Serena Flori –  Nature Communications

Evolutionary radiation of lanthipeptides in marine cyanobacteria – Andres Cubillos-Ruiz –  PNAS

Using Captain Scott’s Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years? – Anne D. Jungblut – Proceedings of the Royal Society B

Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs – Pedro J. Cabello-Yeves – Frontiers in Microbiology

Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment – Yu Wang – Frontiers in Microbiology

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes – Tatsuhiko Hoshino – Frontiers in Microbiology
Phages and viruses

Effect of acute predation with bacteriophage on intermicrobial aggression by Pseudomonas aeruginosa – Patrick R. Secor
Bioinformatics

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data – Gerben Menschaert –

Microbes in the news 

Zombie bacteria and viruses in melting permafrost are waking up  

ExxonMobil and Synthetic Genomics Report Breakthrough in Algae Biofuel Research

Gut microbiome changes linked to numerous biomarkers of type 2 diabetes 

Funky tasting beer? Biofilms may be to blame, MSU researchers say

Bacteria in Your Coughs And Sneezes Can Stay Alive in The Air For Up to 45 Minutes

Microbes on the market

This Company Uses the Human Microbiome to Discover New Disease Mechanisms

June 16, 2017

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Gut microbiome focus: Differences in the gut microbiome between children and adults can mediate the metabolism of arsenic possibly leading to differences in exposure risk, the gut microbiome’s ability to protect against salmonella infection is dependent on the IFNy producing bacteria, the microbiome of insoluble fibre is characterized, and a new in vitro technique to interrogate intestinal transport of microbiota and antigens. Plus an overview of the world data centre for microorganisms, and MicroScope for microbial genome annotation. 

  • Events and jobs

Microbiology Technologist OR Microbiology Medical Technologist – Orlando Florida  

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  • General microbiome

Conference: Current concepts in chronic inflammatory diseases: Interactions between microbes, cellular metabolism, and inflammation – Holger Garn – Allergy and Clinical Immunology

  • Human oral microbiome

Characterisation of Roseomonas mucosa isolated from the root canal of an infected tooth – Nina Diesendorf – BMC Research Notes

  • Human gut microbiome

* Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model – Naiyi Yin – Chemosphere

* Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome – Kim De Paepe – Environmental Microbiology

Review: Microbiota Therapy for Clostridium difficile and Antibiotic Resistant Enteric Infections – Brittany Lewis – Annual Review of Microbiology

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  • Animal experiments

* Enhancement of IFNγ Production by Distinct Commensals Ameliorates Salmonella-Induced Disease – Sophie Thiemann – Cell Host and Microbe

Efficacy of antibiotic treatment of implant-associated Staphylococcus aureus infections with moxifloxacin, flucloxacillin, rifampin, and combination therapy: an animal study – Felix Greimel – Drug Design, Development and Therapy

The scales of the zebrafish: host–microbiota interactions from proteins to populations – Adam Burns – Current Opinion in Microbiology

IL-17 Receptor A Maintains and Protects the Skin Barrier To Prevent Allergic Skin Inflammation – Achilleas Floudas – The Journal of Immunology

Irf4-dependent CD103+CD11b+ dendritic cells and the intestinal microbiome regulate monocyte and macrophage activation and intestinal peristalsis in postoperative ileus – Judith-Mira Pohl – Gut

  • Animal microbiome

Effect of three lactobacilli with strain-specific activities on the growth performance, faecal microbiota and ileum mucosa proteomics of piglets – Yating Su – Journal of Animal Science and Biotechnology

  • Plant, root, and soil microbiome

Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis – Cameron Habib – PLOSone

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function – Sebastian Flues – Environmental Microbiology

Green alder (Alnus viridis) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently – G Schwob – Environmental Microbiology

The role of organic acids on microbial deterioration in the Radix pseudostellariae rhizosphere under continuous monoculture regimes – Hongmiao Wu – Scientific Reports

Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization – María Eugenia Salas – Environmental Microbiology

  • Water and extremophile microbiome

Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean – SJ Goldberg – Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment, and water bacterial communities – Arthur Escalas – Environmental Microbiology

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  • Phages and viruses

Preprint: Bacteria defend against phages through type IV pilus glycosylation – Hanjeong Harvey- bioRxiv

  • Techniques

Dissecting the human microbiome with single-cell genomics – Andrew Tolonen – Genome Medicine

* A human intestinal M-cell-like model for investigating particle, antigen and microorganism translocation – Ana Beloqui – Nature Protocols

  • Metagenomics

* World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide – Linhuan Wu – Nucleic Acids Research

* MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes – David Vallenet – Nucleic Acids Research

Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome – Fergus Collins – Scientific Reports

Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil – Leli Tang – Gene

  • Microbial Physiology

Preprint: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli – Paramita Sarkar – bioRxiv

Preprint: Campylobacter jejuni transcriptome changes during loss of culturability in water – Christina Bronowski – bioRxiv

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  • Microbes in the news

You Are What You Eat, And What You Eat Is Millions of Microbes – Kyle Frischkorn – Smithsonian.com

John Bartlett’s Take on Critical Infectious Disease Topics: Part 3 – John Bartlett – Medscape

Placental Microbiome – Sally Robertson – Life Sciences News

Light-activated bacteria protect rats from heart attacks – Michael Price – Science

These light-eating bacteria could one day help us survive heart attacks – Alessandra Potenza – The Verge

Scientists image molecular machinery never before seen in bacteria – Brooke Hays – UPI

June 14, 2017

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Still quite a few articles on rhizosphere, and antibiotic resistance remains a hot topic, both in the literature and media. How about a Micro-lympics?

Jobs

Microbiology Technician – Seattle Washington

Events

*Annual Microbiology Retreat µlympics – Indiana University

General microbiology

*Commentary: History of Medicine: Origin of the Term Microbiome and why it Matters – Susan L. Prescott – Human Microbiome Journal

A Stoichioproteomic Analysis of Samples from the Human Microbiome Project – Briana Vecchio-Pagan – Frontiers in Microbiology

Adaptor protein mediates dynamic pump assembly for bacterial metal efflux – Ace George Santiago et al. – PNAS

Press: E. coli bacteria’s defense secret revealed – Bill Steele – Phys.org

Uncharacterized bacterial structures revealed by electron cryotomography – Megan J. Dobro et al. – Journal of Bacteriology

Press: Researchers discover new structures in bacteria, seek to determine function – Phys.org

Microbots decorated with silver nanoparticles kill bacteria in aqueous media – Diana Vilela et al. – Applied Materials and Interfaces

Human gut microbiome

Book chapter: The gut microbiome and inflammatory bowel disease – Maire A. Conrad et al. – Pediatric Inflammatory Bowel Disease (Ed. Petar Mamula et al.)

Quantitative systems pharmacology and the personalized drug-microbiota-diet axis – Ines Thiele et al. – Current Opinion in Systems Biology

Human nearly-sterile sites

Endometrial microbiota—new player in town – Inmaculada Moreno & Jason M. Franasiak – Fertility and Sterility

Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women – Luisa F. Gomez-Arango et al. – Scientific Reports

Plant, root and soil microbiome

Stability and dynamics of enzyme activity patterns in the rice rhizosphere: Effects of plant growth and temperature – Tida Ge et al. – Soil Biology and Biochemistry

Doctoral thesis: Exploring candidate genes and rhizosphere microbiome in relation to iron cycling in Andean potatoes – Hua Xiao – Virginia Tech

Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac – Jinping Wu et al. – World Journal of Microbiology and Biotechnology

*Fishing bacteria with a nanonet – F. De Cesare et al. – Materials Today

Isolation, identification, characterization, and screening of rhizospheric bacteria for herbicidal activity – Charles Oluwaseun Adetunji et al. – Organic Agriculture

Bacterial communities on wheat grown under long-term conventional tillage and no-till in the Pacific Northwest of the US – Chuntao Yin et al. – Phytobiomes

*Dispersal enhances beta diversity in nectar microbes – Rachel L. Vannette & Tadashi Fukami – Ecology Letters

Temporal dynamics of soil microbial communities below the seedbed under two contrasting tillage regimes – Florine Degrune et al. – Frontiers in Microbiology

Water and extremophile microbiome

Effect of phosphate-solubilizing bacteria on phosphorus dynamics and the bacterial community during composting of sugarcane industry waste – German A. Estrada-Bonilla et al. – Systematic and Applied Microbiology

Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor – Noah Stern et al. – Applied and Environmental Microbiology

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms – I.L. Angell et al. – Letters in Applied Microbiology

Built environment

The bacterial composition of ventilation filter dust in Norwegian pre-school nurseries – Anders B Nygaard & Colin Charnock – Indoor and Built Environment

Factors Determining the Biodiversity of Halophilic Microorganisms on Historic Masonry Buildings – Anna Otlewska et al. – Microbes and Environments

Phages and viruses

The pepper virome: natural co-infection of diverse viruses and their quasispecies – Yeonhwa Jo et al. – BMC Genomics

Bioinformatics

A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni et al. – Journal of Microbiological Methods

*PrePrint: Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software – Alexander Sczyrba et al. – bioRxiv

Microbes in the news

Live antibiotics use bacteria to kill bacteria – Elizabeth Eaton – Science News

Will a New Drug to Fight Antibiotic Resistant Bacteria Really Work? – Shawn Radcliffe – Healthline news

Former Pfizer Scientist Is Resurrecting Projects To Solve The Multidrug Resistant Bacteria Problem – John LaMattina – Forbes

The Algae That Devastated Florida’s Coasts Also Contained 28 Kinds Of Bacteria, Study Finds – Kate Stein – WGCU

Microbes on the market

DoggyBiome: studying the microbiome to improve dog health – AnimalBiome – Backerkit

Science, career and publishing

Book chapter: Women of Science – Laura E. Willis – Viewpoints on Media Effects: Pseudo-reality and Its Influence on Media Consumers (Ed. Carol M. Madere)

PrePrint: An elective course for medical students on innovation and entrepreneurship – Erik Reinertsen et al. – bioRxiv

June 13, 2017

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Excellent reviews across all sections, with many from the Nature Journals. Also, multiple articles on the tree of life and animal experiments.

General microbiome
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life – Supratim Mukherjee – Nature Biotechnology

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes – Violette Da Cunha – PLoS Genetics

Review: Natural Products and the Gene Cluster Revolution – Paul R. Jensen – Trends in Microbiology

Pregnancy and early life
Review: How nutrition and the maternal microbiota shape the neonatal immune system – Andrew J. MacPherson – Nature Reviews Immunology

Multi-site human microbiome
Review: Role of oral and gut microbiome in nitric oxide mediated colon motility – Miriam Y. Walker – Nitric Oxide

Human skin microbiome
Review: Chemical signaling in mosquito–host interactions: the role of human skin microbiota – William Takken – Current Opinion in Insect Science

Human oral microbiome
Reduced Susceptibility to Antiseptics Is Conferred by Heterologous Housekeeping Genes – Supathep Tansirichaiya – Microbial Drug Resistance

Human gut microbiome
*Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae – Derrick R. Samuelson – PLoS Pathogens

Review: Fungal dysbiosis: immunity and interactions at mucosal barriers – Ilian D. Iliev – Nature Reviews Immunology

Review: Transmission of the gut microbiota: spreading of health – Hilary P. Browne – Nature Reviews Microbiology

Editorial: Post-dieting weight gain: the role of persistent microbiome changes – Christoph A Thaiss – Future Microbiology

Animal experiments
*Thermoneutral housing exacerbates nonalcoholic fatty liver disease in mice and allows for sex-independent disease modeling – Daniel A. Giles – Nature Medicine

*Cold-induced conversion of cholesterol to bile acids in mice shapes the gut microbiome and promotes adaptive thermogenesis – A. Worthmann – Nature Medicine

Integrated Metagenomic Analyses of the Rumen Microbiome of Cattles Reveals Key Biological Mechanisms Associated with Methane Traits – Haiying Wang – Methods

Long-term multi-species Lactobacillus and Bifidobacterium dietary supplement enhances memory and changes regional brain metabolites in middle-aged rats – Caroline O’Hagan – Neurobiology of Learning and Memory

Soy compared with milk protein in a Western diet changes fecal microbiota and decreases hepatic steatosis in obese OLETF rats – Matthew R. Panasevich – Journal of Nutritional Biochemistry

Targeted metabolomics analysis of aromatic amino acids and their gut microbiota-host co-metabolites in rat serum and urine by liquid chromatography with tandem mass spectrometry – Yifeng Zeng – Journal of Separation Science

Effect of cocoa’s theobromine on intestinal microbiota of rats – Sandra Martin-Pelaez – Molecular Nutrition and Food Research

Water and extremophile microbiome
Review: Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems – Alan W. Decho – Frontiers in Microbiology

Review: Linking genes to microbial biogeochemical cycling: lessons from arsenic – Yong-Guan Zhu – Environmental Science and Technology

Food microbiology
Review: Extremozymes from metagenome: Potential applications in food processing – Mahejibin Khan – Critical Reviews in Food Science and Nutrition

Phages and viruses
Review: Interplay between viruses and bacterial microbiota in cancer development – Dariia Vyshenska – Seminars in Immunology

Bioinformatics
A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni – Journal of Microbiological Methods

Power and sample size calculations for high-throughput sequencing-based experiments – Chung-I Li – Briefings in Bioinformatics
Only a short section on microbiome.

Techniques
*A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis – Spencer R. Scott – Nature Microbiology

Body fluid prediction from microbial patterns for forensic application – Eirik Nataas Hanssen – Forensic Science International: Genetics

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinIONTM portable nanopore sequencer – Alfonso Benítez-Páez – GigaScience

Review: Phenotyping of gut microbiota: Focus on capillary electrophoresis – Manuel Ferrer – Electrophoresis

Review: Panacea in progress: CRISPR and the future of its biological research introduction – Michael Carroll – Microbiological Research