Events and jobs

Head Of Bioinformatics – Commense Health

Postdoctoral Research Assistant in Structural Cell Biology of Bacterial Biofilm Formation – University of Oxford – Apply by February 3, 2017

Postdoctoral Research Position in Experimental Microbiome Research – The Ohio State University

General microbiome

*Review Life history and eco-evolutionary dynamics in light of the gut microbiota – Emilie Macke – OIKOS

Pregnancy and early life

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery – Derrick M Chu – Nature Medicine

Method of birth does not effect microbiome composition – Dipali Pathak – Baylor College of Medicine  

Human gut microbiome

*Review The gut-brain axis: is intestinal inflammation a silent driver of Parkinson’s disease pathogenesis? – Madelyn C. Houser – npj Parkinson’s Disease

Animal microbiome

Structure, and culture and predicted function of the gut microbiome of the Mormon cricket Anabrus simplex (Orthoptera: Tettigoniidae)  – Chad C Smith – bioRxiv

Composition of Gut Microbiota in the Gibel Carp (Carassius auratus gibelio) Varies with Host Development – Xinghao Li – Microbial Ecology

Variation in Metabolite Profiles of Amphibian Skin Bacterial Communities Across Elevations in the Neotropics – Daniel Medina – Microbial Ecology

Plant, root, and soil microbiome

Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe – Lauren C. Cline – Ecology Letters

Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants – Abdul Samad – Environmental Microbiology

Soil microbial communities in cucumber monoculture and rotation systems and their feedback effects on cucumber seedling growth – Xingang Zhou – Plant and Soil

Soil bacterial communities and ecosystem functioning change more strongly with season than habitat in a restored floodplain – Emanuela Samaritani – Applied Soil Ecology

Water and extremophile microbiome

Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō‘ihi Seamount – Jarrod J. Scott – Environmental Microbiology

Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan – Arshia Amin – Microbial Ecology

*Editorial Editorial: Geomicrobes: life in terrestrial deep subsurface – Malin Bomberg – Frontiers in Microbiology

Phages and viruses

Newly isolated Nodularia phage influences cyanobacterial community dynamics – S. E. Coloma – Environmental Microbiology

Bioinformatics

MetaSort untangles metagenome assembly by reducing microbial community complexity – Peifeng Ji – Nature Communications

A Dirichlet-tree multinomial regression model for associating dietary nutrients with gut microorganisms – Tao Wang – Biometrics

Bayesian latent variable models for hierarchical clustered count outcomes with repeated measures in microbiome studies – Lizhen Xu – Genetic Epidemiology  

Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer – Qian Zhang – Scientific Reports

VirusSeeker, a computational pipeline for virus discovery and virome composition analysis – Guoyan Zhao – Virology  

Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes – Mohammadkarim Saeedghalati – PLoS Computational Biology

Techniques

Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform – Madhura Castelino – BMC Microbiology

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture – Connor B. Driscoll – Standards in Genomic Sciences

*Review Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease – Bernando Petriz – Frontiers in Chemistry

Microbes in the news

Uncultivated microbes reveal new CRISPR–Cas systems – Ross Cloney – Nature Reviews Genetics

The Cervicovaginal Microbiome May Wield Influence Against HIV Acquisition – Charles B. Hicks, MD –  NEJM Journal Watch

Microbes on the market

RondinX Expands its Microbiome Computational Platform for Drug Development with a Unified Reference Range of Bacterial Dynamics Based on Database of 1,400 Healthy Individuals – Business Wire

Microbiome modeling with Gusto – Juliet Preston – MedCity News

Jobs and Grants
Assistant Research Professor in Microbiome Bioinformatics – University of Oklahoma – Apply by January 31

Assistant Professor of Horticulture (Plant Microbiome Research) – University of Kentucky

Michael Davidson and Roger Tsien Commemorative Travel Awards – Apply by January 31 – Open to masters/PhD students and postdocs traveling to an academic conference in 2017 who can demonstrate that fluorescent proteins have/will have an impact on their research

American Public Health Laboratories (APHL)-CDC Fellowships
Infectious Diseases – Due February 17
Bioinformatics – Due February 28
Antimicrobial Resistance – Due February 28

General microbiome
*Opinion: Host–microbiota interactions: epigenomic regulation – Vivienne Woo – Current Opinion in Immunology

Human gut microbiome
Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases – Chun-Jun Guo – Cell

A case of pyometrocolpos with Bifidobacterium species – Maanasa M. Bhaskar – Anaerobe

*Review: Gut microbiota: A player in aging and a target for anti-aging intervention – Alexander M. Vaiserman – Ageing Research Reviews

Microbiome remodeling via the montmorillonite adsorption-excretion axis prevents obesity-related metabolic disorders – Pengfei Xu – EBioMedicine

Animal experiments
The Bactericidal Lectin RegIIIβ Prolongs Gut Colonization and Enteropathy in the Streptomycin Mouse Model for Salmonella Diarrhea – Tsuyoshi Miki – Cell Host and Microbe

Composition of Gut Microbiota in the Gibel Carp (Carassius auratus gibelio) Varies with Host Development – Xinghao Li – Microbial Ecology

Effects of gut microbiota on the microRNA and mRNA expression in the hippocampus of mice – Jian-jun Chen – Behavioural Brain Research

Plant, root, and soil microbiome
From Microhabitat of Floral Nectar Up to Biogeographic Scale: Novel Insights on Neutral and Niche Bacterial Assemblies – Yana Aizenberg-Gershtein – Environmental Microbiology

Microbial changes linked to the accelerated degradation of the herbicide atrazine in a range of temperate soils – R.L. Yale – Environmental Science and Pollution Research

Microbial siderophores and root exudates enhanced goethite dissolution and Fe/As uptake by As-hyperaccumulator Pteris vittata – Xue Liu – Environmental Pollution

Water and extremophile microbiome
Influence of silver nanoparticles on benthic oxygen consumption of microbial communities in freshwater sediments determined by microelectrodes – Lingzhan Miao – Environmental Pollution

Built environment
Heterogenic response of prokaryotes toward silver nanoparticles and ions is facilitated by phenotypes and attachment of silver aggregates to cell surfaces – Yuting Guo – Cytometry

Phages and viruses
The use of bacteriophages to biocontrol oral biofilms – Szymon P. Szafrański – Journal of Biotechnology

Bioinformatics
A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions – Satomi Mitsuhashi – bioRxiv

A fast and robust protocol for metataxonomic analysis using RNAseq data – Jeremy W. Cox – Microbiome

Microbes in the news
Scientists have caught viruses talking to each other—and that could be the key to a new age of anti-viral drugs – Akshat Rathi – Quartz

Bacteria powered battery built on sheet of paper – Tim Sandle – Digital Journal

Molecule shows ability to thwart pathogens’ genetic resistance to antibiotic – Oregon State University
The original paper is here: Peptide-conjugated phosphorodiamidate morpholino oligomer (PPMO) restores carbapenem susceptibility to NDM-1-positive pathogens in vitro and in vivo – Erin K. Sully – Journal of Antimicrobial Chemotherapy

Andrew Wakefield appearance at Trump inaugural ball triggers social media backlash – Casey Ross – STAT News

Science, publishing, and career
Gates Foundation research can’t be published in top journals – Richard Van Noorden – Nature

Non-microbiology picks
Could a Neuroscientist Understand a Microprocessor? – Eric Jonas – PLoS Computational Biology
Interesting to consider since there are parallels in microbiome analyses!

Events and Jobs

MS in Microbiology & Cell Science from the University of Florida

QC analyst II-Microbiology

Medical Lab Assistant in Microbiology Essex BMS

General microbiome

*Review: Host-microbiota interactions: epigenomic regulation-Vivienne Woo-Current Opinion in Immunology

The emerging importance and challenges of the human mycobiome-Heidi H. Kong-Virulence

Human respiratory microbiome

*Review: Microbiomes in respiratory health and disease: an Asian-Pacific perspective-Sanjay H. Chotirmall-Respirology

Extracellular vesicles, a key mediator to link environmental microbiota to airway immunity-Youngwoo Choi-Allergy, Asthma and Immunology Research

The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia-Tetyana Zakharkina-Thorax

Human skin microbiome

Experimental metagenomics and ribosomal profiling of the human skin microbiome-Pamela Ferretti-Experimental Dermatology

Human nearly-sterile sites

The gut-brain axis in healthy females: lack of significant association between microbial composition and diversity with psychiatric measures-Susan C. Kleiman-PLoS One

Characterization of microbial communities within aggressive prostate cancer tissues-Melissa A. Yow-Infectious Agents and Cancer

Human gut microbiome

A highly active endo-levanase BT1760 of a dominant mammaliam gut commensal Bacteroides thetaiotaomicron cleaves not only various bacterial levans, but also levan of timothy grass-Karin Mardo-PLoS One

Treatment of recurrent Clostridium difficile infection using fecal microbiota transplantation in patients with inflammatory bowel disease-Krista M. Newman-Gut Microbes

Animal experiments

Effect of Vanadium and Tea Polyphenols on Intestinal Morphology, Microflora and Short-Chain Fatty Acid Profile of Laying Hens-Z.H. Yuan-Biological Trace Element Research

Characterization of gut microbiome dynamics in developing pekin ducks and impact of management system-Aaron A. Best-Frontiers in Microbiology

Animal microbiome

Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacterium rodentium-Laura M. Cox-International Journal of Systematic and Evolutionary Microbiology

Plant, root and soil microbiome

Soil microbiome is more heterogeneous in organic than in conventional farming system-Manoeli Lupatini-Frontiers in Microbiology

Development of a method for detection and quantification of B. brongniartii and B. bassiana in soil-L. Canfora-Scientific Reports

Probiotics/prebiotics

Can probiotics modulate human disease by impacting intestinal barrier function?-Peter A. Braun-British Journal of Nutrition

Mulberry anthocyanin biotransformation by intestinal probiotics-Jing-Rong Cheng-Food Chemistry

Phages and viruses

Low-level predation by lytic phage philPLA-RODI promotes biofilm formation and triggers the stringent response in Staphylococcus aureus-Lucia Fernandez-Scientific Reports

Microbes in the news

Seeking structure with metagenome sequences-phys.org

FishTaco method pinpoints bacterial species responsible for each functional imbalance in microbiome-News Medical Life Sciences

What does your armpit say abou you? Museum exhibit takes a look-Corbie Hill-The News & Observer

Is your diet changing your gut bacteria?-Robin Arora-Desilit- Yahoo News

Symbiont-derived antimicrobials contribute to the control of the lepidopteran gut microbiota-Yongqi Shao-Cell Chemical Biology

Hypertension opens the flood gates to the gut microbiota-W. Robert Taylor-Circulation Research

Moth gut bacteria could help create new antibiotics-Claire Maldarelli-Raw Story

New £5 Notes Are Riddled With Bacteria – But It’s The Good Kind-Holly Brockwell-Gizmodo

80 million bacteria are exchanged with each kiss-Humanitas University

Study shows how bacteria can lessen the body’s defenses-Amy Wallace-UPI

Study ties inflammation, gut bacteria to type I diabetes-Serena Gordon-UPI

Pollen has a microbiome. The mode of birth and breastfed status correlates with alterations in the gut microbiome and urine metabolome of children. A catalog of the gut microbiome of the Tyrolean Iceman and ancient bacteria strains. And, the first evidence that phages coordinate their lysis–lysogeny (active-dormant) phases with each other, and even inter-generationally, via small molecule signalling.

• Events and jobs

Lab Technician – Microbiology – GMP – Cambridge – £16k – New Scientist

Podcast: Gut Bacteria and Parkinson’s Connection – Maggie McGuire Kuhl – The Michael J Fox Foundation for Parkinson’s Research

• General microbiome

Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age – Gabriele Andrea Lugli – Microbiome

• Pregnancy and early life

Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort – Cian J. Hill – Microbiome

Oral colostrum priming shortens hospitalization without changing the immunomicrobial milieu – J Romano-Keeler – Journal of Perinatology

• Multi-site human microbiome

Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease – Johanna Klughammer – PLOSone

• Human respiratory microbiome

The effect of cigarette smoking on the oral and nasal microbiota – Guoqin Yu – Microbiome

Bacterial community collapse: a meta-analysis of the sinonasal microbiota in chronic rhinosinusitis – Brett Wagner Mackenzie – Environmental Microbiology

• Human skin microbiome

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

• Human gut microbiome

Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals – M. Andrea Azcarate-Peril – PNAS

• Animal experiments

Drosophila Genotype Influences Commensal Bacterial Levels – Angela M. Early – PLOSone

Lactobacillus rhamnosus GR-1 Attenuates Induction of Hypertrophy in Cardiomyocytes but not through Secreted Protein MSP-1 (p75) – Grace Ettinger – PLOSone

• Animal microbiome

Happens in the best of subfamilies: establishment and repeated replacements of co-obligate secondary endosymbionts within Lachninae aphids – Alejandro Manzano-Marín – Environmental Microbiology

Evolution of new sex chromosomes by lateral genome transfer of bacterial symbiont in pillbug – Richard Cordaux – Journal 2016 International Congress of Entomology

• Plant, root, and soil microbiome

Pollen has a microbiome: implications for plant reproduction, insect pollination and human allergies – Michael Zasloff – Evironmental Microbiology

Phosphorus acquisition efficiency in arbuscular mycorrhizal maize is correlated with the abundance of root-external hyphae and the accumulation of transcripts encoding PHT1 phosphate transporters – Ruairidh J. H. Sawers – New Phytologist

• Water and extremophile microbiome 

Coastal bacterioplankton community response to diatom-derived polysaccharide microgels – Joe D Taylor – Environmental Microbiology Reports

Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean – Wenxue Wu – Environmental Microbiology

• Built environment

Effect of temperature and colonization of Legionella pneumophila and Vermamoeba vermiformis on bacterial community composition of copper drinking water biofilms – Helen Y. Buse – Microbial Biotechnology

• Phages and viruses

Communication between viruses guides lysis–lysogeny decisions – Zohar Erez – Nature

• Bioinformatics and Databases

Data from: Network structure and local adaptation in coevolving bacteria-phage interactions – Gurney J, Aldakak – Dryad Digital Repository

• Techniques

Optical sorting and cultivation of denitrifying anaerobic methane oxidation archaea – Xiaoqiong Qi – Biomedical Optics Express

• Microbes in the news 

Friends for life: human microbiota – E.M. Bik – uBiome

Advancing Phage Therapy  -Joanna Urban – American Society for Microbiology

Bacteria-Treated Mosquitoes Released in More Locations – Kerry Grens – The Scientist

Asgard Archaea Hint at Eukaryotic Origins – Joshua A. Krisch – The Scientist

UNC researchers lead study of prebiotic recomposition in gut microbiome for lactose intolerance – Life Science Daily News Desk

Breastmilk crucial to aid premature C-section babies – Joyce Fegan – Irish Examiner

New study provides insight into fighting drug-resistant bacteria – Isabelle Doan – The Chronicle

Snow microbes used in art – Matt Brooks – WTHITV10

• Microbes on the market 

Rebiotix, Mayo Team Up To Test Orally-Administered Gut Microbe Transplant – Don Jacobson – Twin Cities Business