March 20, 2017

There were almost no papers this weekend, so today’s digest is short.

Events and jobs

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

Postdoctoral Scientist – Microbiome, Mycobiome, Mucosal Immunology – Weill Cornell Medicine, New York City

Water and extremophile microbiome

Whole community metagenomics in two different anammox configurations: process performance and community structure – Ananda S. Bhattacharjee – Environmental Science Technology

Phages and viruses

All of today’s posts are genome announcements:
Genomic Characterization of Three Melon Necrotic Spot Viruses Detected in Human Stool Specimens – Rachel Marine – Genome Announcements

Genome Sequence of Cauliflower Mosaic Virus Identified in Earwigs (Doru luteipes) through a Metagenomic Approach – Márcio Tadeu Godinho – Genome Announcements


metaSPAdes: a new versatile metagenomic assembler – Sergey Nurk – Genome Research

Science, publishing, and career

All biology is computational biology – Florian Markowetz – PLoS Biology

No – all biology is not computational biology – Jonathan Eisen – Tree of Life

March 2, 2017

Events and jobs
Postdoctoral Teaching and Learning Fellow in Microbiome Data Analysis – Department of Microbiology and Immunology (MICB) – University of British Columbia

Commercial Support Manager, Probiotics for Human Health & Microbiome – Hørsholm, Denmark – Chr. Hansen

Position in experimental biochemistry including microbiology – University of Warsaw

Microbiology Laboratory Technician – Milwaukee, WI – Aerotek

Human vaginal microbiome
Specific vaginal lactobacilli suppress the inflammation induced by lipopolysaccharide stimulation through downregulation of toll-like receptor 4 expression in human embryonic intestinal epithelial cells – Keisuke Tobita – Bioscience of Microbiota, Food and Health

Human gut microbiome
Editorial: The gut microbiota and psychiatric illness – Glenda MacQueen – Journal of Psychiatry and Neurosciece

Animal experiments
Understanding the mechanisms of zinc bacitracin and avilamycin on animal production: linking gut microbiota and growth performance in chickens – Eduardo Crisol-Martínez – Applied Microbiology and Biotechnology

Transition of the intestinal microbiota of dogs with age – Hiroaki Masuoka – Bioscience of Microbiota, Food and Health

Faecal microbiota transplantation protects against radiation-induced toxicity – Ming Cui – EMBO Molecular Medicine

Animal microbiome
Comparative analysis of gut microbiota of mosquito communities in central Illinois – Ephantus J. Muturi – PLoS Neglected Tropical Diseases

Plant, root, and soil microbiome
Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars – Aaron K Mahoney – Frontiers in Plant Science

Water and extremophile microbiome
Microbial community assembly and evolution in subseafloor sediment – Piotr Starnawski – PNAS

Phylogenetic Diversity and Anti-MRSA Activity of Halotolerant Actinobacteria from sediments in Great Salt Plains, Oklahoma – Ahmed H Gad – bioRxiv

Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective – Danielle VanMensel – Microbial Ecology

Food microbiology
Boswellia serrata resin extract alleviates azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colon tumorigenesis – YC Chou – Molecular Nutrition Food Research

A series of review articles on the FODMAP diet has been published in the most recent issue of the Journal of Gastroenterology and Hepatology
Review: Use of the low-FODMAP diet in inflammatory bowel disease – Peter R Gibson – Journal of Gastroenterology and Hepatology
Review: How to institute the low-FODMAP diet – Jacqueline S Barrett – Journal of Gastroenterology and Hepatology
Review: When the low FODMAP diet does not work – Emma P Halmos – Journal of Gastroenterology and Hepatology
Review: Nutritional, microbiological and psychosocial implications of the low FODMAP diet – Heidi Maria Staudacher – Journal of Gastroenterology and Hepatology

The spxB gene as a target to identify Lactobacillus casei group species in cheese – Maria Luisa Savo Sardaro – Food Microbiology

GMPR: A novel normalization method for microbiome sequencing data – Jun Chen – bioRxiv

Cohesion: A method for quantifying the connectivity of microbial communities – Cristina Herren – bioRxiv

Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation – Nadieh de Jonge – Bioresource Technology

Microbes in the news
How Bacteria Interfere with Insect Reproduction – Ruth Williams – The Scientist
This references two important papers on Wolbachia:
A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility – John F Beckmann – Nature Microbiology
Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility – Daniel P LePage – Nature

Synopsis: Racing Bacteria – Katherine Wright – APS Physics

Meet green bacteria, airport’s eco-friendly toilet cleaners – Times of India

Assessing Host-Microbiota Relationships – Richard A Stein – Genetic Engineering and Biotechnology News

Bacteria from the ancient city of Troy – Caitlin Pepperell – Microbe Post

Gut bacteria determines the beneficial impacts of soy food on heart health – David Templeton – Pittsburgh Post-Gazette

Microbes on the market
Vaginal Microbiota May Affect Tenofovir Applied Intravaginally – John Schieszer – Infectious Disease Advisor

The Human Microbiome: Advancing New Frontiers in a Rapidly Emerging Market – PR Newswire – Yahoo Finance

New research data published in Frontiers in Microbiology confirm the microbiome’s potential to impact plant health – PR Newswire – Yahoo Finance

Microbiome Therapeutics Market Growth, Forecast and Value Chain 2017-2027 – Future Market Insights – OpenPR

Random Science
Editorial: Microbiome yarns: microbiomology of curly and straight hair – Kenneth Timmis – Microbial Biotechnology

February 21, 2017

Events and jobs
Microbiology Analyst Level II – DTS Food Laboratories – Brisbane, AU

Microbial Menagerie is profiling #ActualLivingScientists, especially microbiologists! Visit here for more information, or sign up here!

4th International Symposium on the Environmental Dimension of Antibiotic Resistance – Aug 13-17, 2017 in Lansing, MI

5th Molecular Microbiology Meeting & 4th Midlands Molecular Microbiology Meeting (M4) – Sept 13-14, 2017 in Birmingham, UK

General microbiome
Metagenomic DNA sequencing for the diagnosis of intraocular infections – Thuy Doan – bioRxiv

Human skin microbiome
Bacterial biofilm in chronic lesions of hidradenitis suppurativa – H.C. Ring – British Journal of Dermatology

Human gut microbiome
Review: Bile acid control of metabolism and inflammation in obesity, type 2 diabetes, dyslipidemia and NAFLD – Oscar Chavez-Talavera – Gastroenterology

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli Moss – bioRxiv

Isolation and high-dimensional phenotyping of gastrointestinal immune cells – Bruna A. David – Imumunology
Not focused on microbes – but may be of use to those working with these cells!

Water and extremophile microbiome
Oxygenic and anoxygenic photosynthesis in a microbial mat from an anoxic and sulfidic spring – Dirk de Beer – Environmental Microbiology

A six thousand-year record of climate and land-use change from Mediterranean seagrass mats – Lourdes Lopez-Merino – Journal of Ecology
There is a hidden section on fungi.

High-Throughput Metabolic Network Analysis and Metatranscriptomics of a Cosmopolitan and Streamlined Freshwater Lineage – Joshua J Hamilton – bioRxiv

Are oceanic fronts ecotones? Seasonal changes along the Subtropical Front show fronts as bacterioplankton transition zones but not diversity hotspots – Sergio E Morales – bioRxiv

Built environment
Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings – Sumayah F. Rahman – MicrobiologyOpen

Comparative analysis of metagenomes of Italian top soil improvers – F. Gigiliucci – Environmental Research
This does not seem available yet, so PubMed is linked rather than the paper.

Food microbiology
Diversity analysis and quantification of lactic acid bacteria in traditionally fermented yaks’ milk products from Tibet – Yan Ren – Food Biotechnology

Phages and viruses
Review: Risk of waterborne virus spread – review of survival of relevant fish and crustacean viruses in the aquatic environment and implications for control measures – Birgit Oidtmann – Reviews in Aquaculture

Microbial interactions
Local interactions lead to spatially correlated gene expression levels in bacterial groups – Simon van Vliet – bioRxiv

Science, publishing, and career
Broad Institute prevails in heated dispute over CRISPR patents – Sharon Begley – STAT News, along with six takeaways.

February 14, 2017

Events and jobs
Postdoctoral research fellow in Microbiome Research – Karolinska Institutet

Postdoctoral Scientist ( Microbiome, Mycobiome, Mucosal Immunology) – Jill Roberts Institute for Research in IBD at Weill Cornell Medicine, New York City

Senior Lecturer in Food Microbiology – RMIT Bundoora Campus

Junior Specialist in Environmental Microbiology – University of California, Santa Cruz

General microbiome
Uncharacterized bacterial structures revealed by electron cryotomography – Megan J Dobro – bioRxiv

Pregnancy and early life
Review: Infant fungal communities: current knowledge and research opportunities – Tonya L. Ward – BMC Medicine

Human gut microbiome
A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline – B.J. Levin – Science
Also described in this short article: New tool can help researchers identify enzymes—and their abundance—in microbiomes –

Dynamics of the human gut microbiome in inflammatory bowel disease – Jonas Halfvarson – Nature Microbiology

Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant – Maryam Tidjani Alou – Antonie van Leewenhoek

Animal microbiome
The microbiome of bulk tank milk: Characterization and associations with somatic cell count and bacterial count – M.X. Rodrigues – Journal of Dairy Science

Dynamics of the microbiota found in the vaginas of dairy cows during the transition period: Associations with uterine diseases and reproductive outcome – M.L.S. Bicalho – Journal of Dairy Science

Prophylactic use of a standardized botanical extract for the prevention of naturally occurring diarrhea in newborn Holstein calves – A.G.V. Teixeira – Journal of Dairy Science

Plant, root, and soil microbiome
Four years of experimental warming do not modify the interaction between subalpine shrub species – Alba Anadon-Rosell – Oecologia

Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria – Md Sainur Samad – bioRxiv

Water and extremophile microbiome
Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process – Andrew R.J. Curson – Nature Microbiology
This is summed up in the short article: Marine bacteria produce an environmentally important molecule with links to climate –

Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment – Chioma C. Obi – Applied Microbiology and Biotechnology

Diversity and community composition of particle-associated and free-living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: Evidence of dispersal limitation in the Bransfield Strait – Mathias Milici – Limnology and Oceanography

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type – R. Heyer – Biotechnology for Biofuels

Probiotics / prebiotics
Chapter One – Antivirulence Properties of Probiotics in Combating Microbial Pathogenesis – M. Surendran Nair – Advances in Applied Microbiology

Reclamation of Chinese herb residues using probiotics and evaluation of their beneficial effect on pathogen infection – Fanjing Meng – Journal of Infection and Public Health

Probiotic dietary supplementation in Nile tilapia as prophylaxis against streptococcosis – M.M. Yamashita – Aquaculture Nutrition

Phages and viruses
Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families – Jemma L. Geoghegan – PLoS Pathogens

Plaques formed by mutagenized viral populations have elevated co-infection frequencies – Elizabeth R. Aguilera – bioRxiv

dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes – Matthew R Olm – bioRxiv

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice – Joao Carlos Gomes-Neto – Journal of Microbiological Methods

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

Microbes in the news
“Archaea” unites University on sesquicentennial – Tess O’Brien – The Daily Illini (student newspaper at University of Illinois)

How to quickly identify sepsis-causing bacteria – melt it down – Lisa-Ann Lee – New Atlas
The paper referenced is Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping – Stephanie I. Fraley – Scientific Reports

Chemical engineers boost bacteria’s productivity –
The paper referenced is Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit – Apoorv Gupta – Nature Biotechnology

Microbes on the market
Human Microbiome Market is Expecting Worldwide Growth by 2020 – Persistence Market Research Study

Ritter Pharmaceuticals Announces Collaboration with University of British Columbia to Explore Development of Microbiome Therapeutics in Environmental Enteropathy – Yahoo Finance

Science, publishing, and career
The Troll Taunter – Andrew McMillen – BackChannel
This is an amazing piece: “But on that Friday night, Temple-Wood had an idea. For every harassing email, death threat, or request for nude photos that she received, she resolved to create a Wikipedia biography on a notable woman scientist who was previously unknown to the free online encyclopedia.”

Do’s and don’ts for scientists who want to shape policy – Erik Stokstad – Science

Scientists should be political but not partisan – Angela de Pace – Medium

January 30, 2017

General microbiome
Commentary: The AGA’s Fecal Microbiota Transplantation National Registry: An important step toward understanding risks and benefits of microbiota therapeutics – Colleen R. Kelly – Gastroenterology

Review: Microbes and Mental Health: A Review – Ryan Rieder – Brain, Behavior, and Immunity

Review: The role of divalent metals for infectious diseases susceptibility and outcome – Guenter Weiss – Clinical Microbiology and Infection

Human gut microbiome
Effects of Acarbose on the Gut Microbiota of Prediabetic Patients: A Randomized, Double-blind, Controlled Crossover Trial – Xiuying Zhang – Diabetes Therapy

Clinical Commentary: More Than a Gut Feeling: The Implications of the Gut Microbiota in Psychiatry – Pochu Ho – Biological Psychiatry

Animal experiments
Target Intestinal Microbiota to Alleviate Disease Progression in Amyotrophic Lateral Sclerosis – Yong-guo Zhang – Clinical Therapeutics

Commensal Bacteria at the Crossroad between Cholestrol Homeostasis and Chronic Inflammation in Atherosclerosis – Kazuyuki Kasahara – Journal of Lipid Research

Bovine milk oligosaccharides decrease gut permeability and improve inflammation and microbial dysbiosis in diet-induced obese mice – Gaelle Boudry – Journal of Dairy Science

Broad spectrum antibiotic enrofloxacin modulates contact sensitivity through gut microbiota in a murine model – Anna Strzepa – Journal of Allergy and Clinical Immunology

Effects of subchronic oral toxic metal exposure on the intestinal microbiota of mice -Qixiao Zhai – Science Bulletin

In vitro fermentation of key dietary compounds with rumen fluid: A genome-centric perspective – Stefano Campanaro – Science of the Total Environment

Cow, yak, and camel milk diets differentially modulated the systemic immunity and fecal microbiota of rats – Wen Yongping – Science Bulletin

Animal microbiome
The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential – Ciro Cesar Rossi – Veterinary Microbiology

Effects of daidzein on performance, serum metabolites, nutrient digestibility, and fecal bacterial community in bull calves – X.H. Zhao – Animal Feed Science and Technology

Plant microbiome
Marchantia liverworts as a proxy to plants basal microbiomes – Luis David Alcaraz – bioRxiv

Water and extremophile microbiome
Microbial succession in biofilms growing on artificial substratum in subtropical freshwater aquaculture ponds  – Zhifei Li – FEMS Microbiology Letters

Model communities hint to promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria – Sarahi L Garcia – bioRxiv

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy – William J. Brazelton – PeerJ

Food microbiology
Beneficial effects of legumes in gut health – Alfonso Clemente – Current Opinion in Food Science

Probiotics / prebiotics
Impact of ageing and a synbiotic on the immune response to seasonal influenza vaccination; a randomised controlled trial – Sumaia Enani – Clinical Nutrition

Antivirulence Properties of Probiotics in Combating Microbial Pathogenesis – M. Surendran Nair – Advances in Applied Microbiology

MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data  – B Fosso – Bioinformatics

Linclust: clustering protein sequences in linear time – Martin Steinegger – bioRxiv

Chapter 3: Best practices for germ-free derivation and gnotobiotic zebrafish husbandry – E. Melancon – Methods in Cell Biology

Chapter 10: Modeling intestinal disorders using zebrafish – X. Zhao – Methods in Cell Biology

A novel LCMSMS method for quantitative measurement of short-chain fatty acids in human stool derivatized with 12C- and 13C-labelled aniline – James Chun Yip Chan – Journal of Pharmaceutical and Biomedical Analysis

Newly Isolated Strains
Actinomyces bouchesdurhonensis sp. nov. and Actinomyces mediterranea sp. nov., isolated from Human Stomach and Duodenum – Morgane Mailhe – Human Microbiome Journal

Peptoniphilus duodeni sp. nov., a new bacterial species identified in human duodenum – Morgane Mailhe – Human Microbiome Journal

Bacteroides bouchesdurhonensis sp. nov., a new bacterium isolated from the human gut – Sokhna Ndongo – Human Microbiome Journal

Microbes in the news
What Even is Kombucha, Anyway? – Anthony Rivas – BuzzFeed

Preventing Biofilm and Bacteria in Dental Operatory Tubing – Tech Featured

Non-Microbiology picks
The State of Systems Genetics in 2017 – Nitin S. Baliga – Cell Systems

Trump’s Immigration Ban Is Already Harming American Science – Ed Yong – The Atlantic

Geneticist launches bid for US Senate – Sara Reardon – Nature

January 23, 2017

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

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!