April 1, 2017

Events and jobs

Asst/Assoc Collegiate-Track Clinical Microbiology Faculty – Virginia Tech

General microbiome

Salivary inflammatory markers and microbiome in normoglycemic lean and obese children compared to obese children with type 2 diabetes – Waleed F. Janem – PLOS ONE

Microbiome study finds children with type 2 diabetes more likely to have poor oral health – Ellen Goldbaum – Medical Xpress

Cross-talk among metabolic parameters, esophageal microbiota, and host gene expression following chronic exposure to an obesogenic diet – Nadeem O. Kaakoush – Scientific Reports

Review: Microbiome Tools for Forensic Science – Jessica L. Metcalf – Trends in Biotechnology

Book: Forensic Microbiology – David O. Carter

Review: The legacy of the past: effects of historical processes on microbial metacommunities – Máté Vass – Aquatic Microbial Ecology

Human respiratory microbiome

The microbiome and secondary lung disease in neuromuscular patients: Is it time to change our clinical practice? – Reply – Florian Stehling – Respirology

Human skin microbiome

Patterns in the skin microbiota differ in children and teenagers between rural and urban environments – Jenni Lehtimäki – Scientific Reports

Human vaginal microbiome

Transient microbiota exposures activate dormant Escherichia coli infection in the bladder and drive severe outcomes of recurrent disease – Nicole M. Gilbert – PLOS Pathogens

Vaginal bacteria can trigger recurrent UTIs, study shows – Science Daily

Human gut microbiome

Review: Diet and microbiota in inflammatory bowel disease: The gut in disharmony – Davy CM Rapozo – World Journal of Gastroenterology

The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level – Wiley Barton – Gut

Animal experiments

NLRP12 regulates gut microbiota to suppress intestinal inflammation – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Community structure of the gut microbiota in sympatric species of wild Drosophila – Vincent G. Martinson – Ecology Letters

Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq – Alexandra Grote – PLOS Neglected Tropical Diseases

Researchers profile symbiotic relationship between bacteria and filarial nematodes – Medical Xpress

The Bacterial Community Found on the surface Purple Martin (Progne subis) Eggs – Beth A. Potter – The Open Ornithology Journal

Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas – Ghaida Hadaidi – Scientific Reports

Plant, root, and soil microbiome

Relationship of microbial communities and suppressiveness of Trichoderma fortified composts for pepper seedlings infected by Phytophthora nicotianae – Margarita Ros – PLOS ONE

Two-year field monitoring shows little evidence that transgenic potato containing ABF3 significantly alters its rhizosphere microbial community structure – Ki Jung Nam – Journal of Ecology and Environment

Members of Gammaproteobacteria as indicator species of healthy banana plants on Fusarium wilt-infested fields in Central America – Martina Köberl – Scientific Reports

Review: From yogurt to yield: Potential applications of lactic acid bacteria in plant production – John R. Lamont – Soil Biology and Biochemistry

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses – Tianzhu Li – PLOS ONE

Water and extremophile microbiome

Impact of selectively enriched microbial communities on long-term fermentative hydrogen production – R.K. Goud – Bioresource Technology

Co-invasion hypothesis explains microbial community structure changes in upland streams affected by riparian invader – Paul J. McInerney – Freshwater Science

Silver nanoparticles uptake by salt marsh plants – Implications for phytoremediation processes and effects in microbial community dynamics – Joana P. Fernandes – Marine Pollution Bulletin

Food microbiology

Identification of Microbial Profile of Koji Using Single Molecule, Real-Time Sequencing Technology – Wenyan Hui – Journal of Food Science

Probiotics / prebiotics

Roles of Probiotic Lactobacilli Inclusion in Helping Piglets Establish Healthy Intestinal Inter-environment for Pathogen Defense – Jiajun Yang – Probiotics and Antimicrobial Proteins

Phages and viruses

Review: Intriguing interaction of bacteriophage-host association: An understanding in the era of omics – Krupa M. Parmar – Frontiers in Microbiology


Review: Are Next-Generation Sequencing Tools Ready for the Cloud? – Antonio Celesti – Trends in Biotechnology


Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP) – Scott Tighe – Journal of Biomolecular Technology

In vitro gene expression-coupled bacterial cell chip for screening species-specific antimicrobial enzymes – Seok-Joon Kwon – Journal of Biotechnology and Bioengineering

Review: International Standards for Genomes, Transcriptomes, and Metagenomes – Christopher E. Mason – Journal of Biomolecular Technology

A comparison of sampling methods for examining the laryngeal microbiome – Alissa S. Hanshew – PLOS ONE

Microbes in the news

Probiotics For Babies: Why Your Baby’s Gut Health Is So Important –  Joy D’Souza – The Huffington Post Canada

NIH Wants to Test New Bacteria Therapy for Eczema – Maggie Fox – NBC News

Microbes on the market

Regulator OKs bacteria’s spread – Martin Cash – Winnipeg Free Press

March 18, 2017

Events and jobs

Research Fellow in Omics analysis – King’s College London – Apply by April 12, 2017

Postdoctoral Research Position in Marine Microbial Ecology – University of Southern Mississippi

General microbiome

Microbial Influences in Cardio–Metabolic Diseases – Rachel Petersen – New York Academy of Sciences

*Review: Microbiota: a key orchestrator of cancer therapy – Soumen Roy – Nature Reviews Cancer

*Review: Caenorhabditis elegans as a model for microbiome research – Fan Zhang – Frontiers in Microbiology

Human respiratory microbiome

The relationship between nasopharyngeal CCL5 and microbiota on disease severity among infants with bronchiolitis – Kohei Hasegawa – Allergy

Human gut microbiome

The Food Contaminant Deoxynivalenol Exacerbates the Genotoxicity of Gut Microbiota – Delphine Payros – mBio

Delayed utilization of some fast-fermenting soluble dietary fibers by human gut microbiota when presented in a mixture – Yunus E. Tuncil – Journal of Functional Foods

Animal experiments

Deciphering the combinatorial influence of diet and the microbiota on experimental colitis – Sean R. Llewellyn – bioRxiv

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – ISME J

Animal microbiome

Comparison of bacterial populations in bedding material, on teat ends, and in milk of cows housed in compost bedded pack barns – R. L. Albino – Animal Production Science

Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis – Elizabeth G. Pringle – Proceedings of the Royal Society Biological Sciences

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment – Till Röthig – Scientific Reports

Plant, root, and soil microbiome

Root microbiota drive direct integration of phosphate stress and immunity – Gabriel Castrillo – Nature

Striking alterations in the soil bacterial community structure and functioning of the biological N cycle induced by Pennisetum setaceum invasion in a semiarid environment – G. Rodríguez-Caballero – Soil Biology and Biochemistry

Plant growth promoting rhizobacteria are more effective under drought: a meta-analysis – Rachel L. Rubin – Plant and Soil

Effect of biodynamic soil amendments on microbial communities in comparison with inorganic fertilization – Sibylle Faust – Applied Soil Ecology

Water and extremophile microbiome

Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico) – Miguel Medrano-Santillana – Extremophiles

Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica) – Rosabruna La Ferla – Microbial Ecology

Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data – Michelle A. Allen – Scientific Reports

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater – Flavia Flaviani – Viruses

Built environment

Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process – Rocio J. Alcántara-Hernández – Letters in Applied Microbiology

Variability of airborne bacteria in an urban Mediterranean area (Thessaloniki, Greece) – Savvas Genitsaris – Atmospheric Environment

*Review: A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities – Caroline De Tender – Analytical Methods


*Review: Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data – Jian Xu – Engineering

*Review: Metaproteomic strategies and applications for gut microbial research – Mingming Xiao – Applied Microbiology and Biotechnology

Microbes in the news

Bacteria-Enriched Lotion Battles Skin Infections – Jenna Flannigan – Live Science

Frozen, Freeze-dried Products for Fecal Microbiota Transplantation as Effective as Fresh? – Pharmacy Times

Study by Irish scientists finds porridge to be good for the heart and gut – RTE

Certain Bacteria Within Gut Microbiome May Halt Inflammation Naturally, Study Says – Patricia Inacio – IBD News Today

Antibiotic overuse might be bad for bees – Mary Beth Griggs – Popular Science

Microbiome research Studies aim to help health, environment – David Wahlberg – The Times Record

My cats poop for science – Jonathan M. Giltin – ars Technica

Microbes on the market

Seres doubles down on a microbiome do-over as the FDA clears a make-or-break study – John Carroll – Endpoint News

Bacteria Hysteria

Revealed: Which supermarket’s chicken is most likely to contain food poisoning bacteria? – Tom Belger – Liverpool Echo

March 4th, 2017

Events and jobs

Head, Microbiome Discovery Research – Johnson & Johnson

Multi-site human microbiome

Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients – Jessica R. Galloway-Peña – Genome Medicine

Human gut microbiome

Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use – K. Korpela – Microbiome

Animal experiments

Metaproteogenomics reveals taxonomic and functional changes between cecal and fecal microbiota in mouse – Alessandro Tanca – Frontiers in Microbiology

Animal microbiome

Cultivable gut bacteria provide a pathway for adaptation of Chrysolina herbacea to Mentha aquatica volatiles – Graziano Pizzolante – BMC Plant Biology

Gut bacteria oversee the special relationship between the green mint leaf beetle and watermint – BMC Series Blog

Effects of tussah immunoreactive substances on growth, immunity, disease resistance against Vibrio splendidus and gut microbiota profile of Apostichopus japonicus – Shuhui Ma – Fish & Shellfish Immunology

Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses – Holly H. Ganz – mSystems

The microbiome of the ant-built home: the microbial communities of a tropical arboreal ant and its nest – Jane Lucas – Ecosphere

*Perspective: Gut microbiome transmission in lizards – Timothy J. Colston – Molecular Ecology

Plant, root, and soil microbiome

Microbial communities in soil chronosequences with distinct parent material: the effect of soil pH and litter quality – Fernando D. Alfaro – Journal of Ecology

Water and extremophile microbiome

Volcanic ash supports a diverse bacterial community in a marine mesocosm – V. Witt – Geobiology

Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment – Martin Taubert – Environmental Microbiology

Built environment

Response of microbial community structure to pre-acclimation strategies in microbial fuel cells for domestic wastewater treatment – Younghyun Park – Bioresource Technology

Food microbiology

Viable microbial loads on citrus carpoplane during packhouse processing and survival of foodborne pathogens in reconstituted postharvest fungicides – A. Gomba – Journal of Food Safety

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage – Lysiane Duniere – BMC Microbiology

Probiotics / prebiotics

Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss) – Ana Teresa Gonçalves – Journal of Applied Microbiology

Exploration of the effect of probiotics supplementation on intestinal microbiota of food allergic mice – Bo Yang – American Journal of Translational Research

Phages and viruses

Human norovirus binding to select bacteria representative of the human gut microbiota – Erin A. Almand – PLoS ONE

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere


REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial
genomes – Elvis Ndah – BioRxiv

Normalization and microbial differential abundance strategies depend upon data characteristics – Sophie Weiss – Microbiome

How conserved are the conserved 16S-rRNA regions? – Marcel Martinez-Porchas – PeerJ

Microbes in the news

Gut bacteria affect intestines and brain in IBS patients – Medical News Today

Intestinal Bacteria Alter Gut and Brain Function – Neuroscience News

Why Are People Sending Poop Through the Mail? For Their Health – GQ Magazine

Microbes on the market

Next-gen microbiome drugs are now on sale, should you buy them? – New Scientist


February 18, 2017

Events and jobs

Assistant Professor – Pathogen and Microbiome Institute at Northern Arizona University

Assistant Professor – Biochem & Microbiology at Rutgers University

Expert Panel Discussions to be Highlight of Agenda at the 3rd Annual Translational Microbiome Conference – prweb

General microbiome

Neutral and niche dynamics in a synthetic microbial community -NJ Cira – bioRxiv

Human respiratory microbiome

Indoor fungal diversity in primary schools may differently influence allergic sensitization and asthma in children – João Cavaleiro Rufo – Pediatric Allergy Immunology

Human gut microbiome

Mining the Human Gut Microbiota for Immunomodulatory Organisms – Naama Geva-Zatorsky – Cell

Animal experiments

The enteric nervous system promotes intestinal health by constraining microbiota composition – Annah S. Rolig – PLoS Biology

Biologists control gut inflammation by altering the abundance of resident bacteria – Science Daily

Drunk bugs: Chronic vapour alcohol exposure induces marked changes in the gut microbiome in mice – Veronica L. Peterson – Behavioural Brain Research

Mouse model of alcohol abuse shows microbiome changes – Taconic

Feeding a High Concentration Diet Induces Unhealthy Alterations in the Composition and Metabolism of Ruminal Microbiota and Host Response in a Goat Model – Canfeng Hua – Frontiers in Microbiology

Animal microbiome

Impact of levels of total digestible nutrients on microbiome, enzyme profile and degradation of feeds in buffalo rumen – Anju Kala – PLoS ONE

Immune system stimulation by the gut symbiont Frischella perrara in the honey bee (Apis mellifera) – Olivier Emery – Molecular Ecology

Integrating gut microbiota immaturity and disease-discriminatory taxa to diagnose the initiation and severity of shrimp disease – Jinbo Xiong – Environmental Microbiology

Plant, root, and soil microbiome

Linking soil biology and chemistry using bacterial isolate exometabolite profiles – Tami L Swenson – bioRxiv

Ecological and conventional viticulture gives rise to distinct fungal and bacterial microbial communities in vineyard soils – M. Likar – Applied Soil Ecology

Effects of land use on soil microbial biomass, activity and community structure at different soil depths in the Danube floodplain – J.P. van Leeuwen – European Journal of Soil Biology

*Review: How do Plants-Having Different Exudation Patterns Shape a Similar Microbial Community? – Pil Y – Journal of Botanical Sciences

Water and extremophile microbiome

Epiphytic bacterial communities of the alga Fucus vesiculosus in oil-contaminated water areas of the Barents Sea – D. V. Pugovkin – Doklady Biological Sciences

Warmer night-time temperature promotes microbial heterotrophic activity and modifies stream sediment community – Anna Freixa – Global Change Biology

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

Built environment

Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor – Allison R. Perrotta – PLoS ONE


*Review: A review of bioinformatics tools for bio-prospecting from metagenomic sequence data – Despoina Deppie Roumpeka – Frontiers in Genetics


Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity – Stanislav S. Terekhov – PNAS

Microbes in the news

From mice, clues to microbiome’s influence on metabolic disease – EurekaAlert

Bacteria Hysteria

Dog parks ground zero for deadly bacteria? How to keep your pet safe from leptospirosis – ABC15

January 24, 2017

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. Housernpj 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


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


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