March 25, 2017

A short Saturday digest for this weekend, featuring a review on dry habitat bacteria published on Nature Reviews Microbiology and an interesting piece on how knowledge of Systems Biology can aid in biochemical production challenges.

General microbiome

Review: Xerotolerant bacteria: surviving through a dry spell
Pedro H. Lebre – Nature Reviews Microbiology

Human gut microbiome

Review: Targeting the Microbiome in Heart Failure
Allyson Zabell, W.H. Wilson Tang – Current Treatment Options in Cardiovascular Medicine

Review: Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia
Sabrina Tamburini & Jose C. Clemente – Nature Reviews Gastroenterology & Hepatology

Temporal dynamics of the gut microbiota in people sharing a confined environment, a 520-day ground-based space simulation, MARS500
Silvia Turroni – Microbiome

Review: Role of the small intestine, colon and microbiota in determining the metabolic fate of polyphenols
Gary Williamson & Michael N. Clifford – Biochemical Pharmacology

Microbial diseases

Review: Pathogenic Mechanisms of Cryptosporidium and Giardia
Gabriela Certad – Trends in Parasitology

Animal microbiome

Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge
Ren-Mao Tian – mSystems

Plant, root, and soil microbiome

Intercropping maize and common bean enhances microbial carbon and nitrogen availability in low phosphorus soil under Mediterranean conditions
Mourad Latati – European Journal of Soil Biology

Antibiotic and Heavy Metal Tolerance of Some Indigenous Bacteria Isolated From Petroleum Contaminated Soil
Jai Godheja – International Journal of Current Microbiology and Applied Sciences

Water, estuarine and marine microbiome

Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment
Daniel F. R. Cleary – Marine Ecology

Metagenomic and Culture-Dependent Analysis of the Bacterial Diversity of a Hot Spring Reservoir as a Function of the Seasonal Variation
B. A. Kikani – International Journal of Environmental Research

Space and extremophile microbiome

Stratosphere Conditions Inactivate Bacterial Endospores from a Mars Spacecraft Assembly Facility
Christina L. Khodadad – Astrobiology

Built environment

Short-term Effects of Great Cormorant Droppings on Water Quality and Microbial Community of an Artificial Agricultural Reservoir
Il Han – Journal of Environmental Quality

Microbial biotechnology

Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw
E. Gozde Ozbayram – Anaerobe

Systems biology solutions for biochemical production challenges
Anne Sofie Lærke Hansen – Current Opinion in Biotechnology

General microbiology

The Pangenome of the genus Clostridium
Zulema Udaondo – Environmental Microbiology

March 16, 2017.

A long review today, lots of environmental microbiome, a few papers on the methods, virus and microbial biotechnology sections and at the end a Nature announcement for transparency policy updates, aiming for better research reproducibility.

Oral Microbiome

Targeting of Streptococcus mutans Biofilms by a Novel Small Molecule Prevents Dental Caries and Preserves the Oral Microbiome
S. S. Garcia – Journal of Dental Research

Human nearly-sterile sites

Review: Microbiome effects on immunity, health and disease in the lung
Shakti D. Shukla – Clinical & Translational Immunology

Animal Microbiome

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle
Sigmund Jensen – Marine Ecology

Animal experiments

Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves
Y. F. Deng – Scientific Reports

Antiprotozoal Effect of Saponins in the Rumen Can Be Enhanced by Chemical Modifications in Their Structure
Eva Ramos-Morales – Frontiers in Microbiology

Plant, root, and soil microbiome

Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylands
Xiao-Bo Wang – The ISME Journal

Phosphate solubilizing microbes: an effective and alternative approach as
Kumar Anand – International Journal of Pharmacy and Pharmaceutical Sciences

Master’s thesis: An Investigation Of The Tri-Trophic Interactions In
The Rhizosphere Of Medicago Truncatula Using A
Functional Microbiome Approach
Amanda Anne Rosier – University of Delaware

Water and extremophile microbiome

Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean—from the Equator to the Bay of Bengal
Jing Wang – Frontiers in Microbiology

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis
Niranjan Nitin Parulekar – PlOS One

Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment
Daniel F. R. Cleary – Marine Ecology

Built environment

Impact of water heater temperature setting and water use frequency on the building plumbing microbiome
Pan Ji – The ISME Journal

Food microbiology

Effects of cellulase-producing bacteria on bacterial community structure and diversity during fermentation of Chinese liquor grains
J. H. Guo – The Journal of The Institute of Brewing

Microbial Biotechnology

The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors
Shelesh Agrawal – Microbiology Open

Diversity of Cultivable Protease-Producing Bacteria in Laizhou Bay Sediments, Bohai Sea, China
Yan Li – Frontiers in Microbiology

General Microbiology

Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria
Masahiro Kanno – Nature Communications

Short communication: Membrane vesicle-mediated bacterial communication
Masanori Toyofuku – The ISME Journal

Brief Report: Influence of the alginate production on cell-to-cell communication in Pseudomonas aeruginosa PAO1
Jiayue Yang – Environmental Microbiology Reports

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio
Anne-Catherine Ahn – PlOS One

Review article: The Potential of Systems Biology to Discover Antibacterial Mechanisms of Plant Phenolics
Caroline S. Rempe – Frontiers in Microbiology

Phages and viruses

Mini-Review: Driving HIV-1 into a Vulnerable Corner by Taking Advantage of Viral Adaptation and Evolution
Shigeyoshi Harada – Frontiers in Microbiology

Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome
Daniel Aguirre de Cárcer – PlOS One

Review: The concept of commensal viruses almost 20 years later: redefining borders in clinical virology
Diem-Lan Vu & Laurent Kaiser – Clinical Microbiology and Infection

Statistics / Bioinformatics

A fast small-sample kernel independence test for microbiome community-level association analysis
Xiang Zhan – Biometrics

Revealing large metagenomic regions through long DNA fragment hybridization capture
Cyrielle Gasc & Pierre Peyret – Microbiome

Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies
Sara Ciucci – Scientific Reports

Microbes in the news

Snow Bacteria, A Pandora’s Box? – GlacierHub

Phage therapy shown to kill drug-resistant superbug (link to original paper included) – HealthCanal

A Microbe Hunter Plies Her Trade In Space – NPR

Science, publishing, and career

Announcement: Transparency upgrade for Nature journals – Nature

March 13, 2017.

Quite a few picks from Nature Reviews Microbiology as a fresh issue was released today. We also see some nice papers on microbial diseases. The post author’s highlight today goes to the interesting review from Thurber et al. on the virus section: Virus–host interactions and their roles in coral reef health and disease. Have a great week!

General microbiome

Review: Timing the day: what makes bacterial clocks tick?
Carl Hirschie Johnson – Nature Reviews Microbiology

Microbial diseases

Evolutionary Constraints on the Norovirus Pandemic Variant GII.4_2006b over the Five-Year Persistence in Japan.
Hironori Sato – Frontiers in Microbiology

Review: Anti-trypanosomatid drug discovery: an ongoing challenge and a continuing need Mark C. Field – Nature Reviews Microbiology

Commentary: The chicken or the egg? Changes in oral microbiota as cause or consequence of mucositis during radiation therapy
Stephen T. Sonis – EBioMedicine

Commentary: From bugs to brains: The microbiome in neurological health
Kyla A. McKay – Multiple Sclerosis and Related Disorders

Commentary: A Microbiome Foundation for the Study of Crohn’s Disease
Dirk Gevers – Cell Host & Microbe

Human gut microbiome

European consensus conference on faecal microbiota transplantation in clinical practice
Giovanni Cammarota – Gut

Commentary: Microbe Hunting Hits Home
Ivaylo I. Ivanov – Cell Host & Microbe

Commentary: Microbes and Diet-Induced Obesity: Fast, Cheap, and Out of Control
Peter J. Turnbaugh – Cell Host & Microbe

Review: The gut microbiome and microbial translocation in multiple sclerosis
Ali Mirza – Clinical Immunology

Plant, root, and soil microbiome

COREXIT 9500 enhances oil biodegradation and changes microbial community structure of oil-enriched microcosms
Techtmann SM – Applied Environmental Microbiology

Soil formation and initial microbiological activity on a foreland of an Arctic glacier (SW Svalbard)
Dorota Górniak – Applied Soil Ecology

The response of soil microbial diversity and abundance to long-term application of biosolids
Abdul-Wahab Mossa – Environmental Pollution

Comparative analysis of metagenomes of Italian top soil improvers
Federica Gigliucci – Environmental Research

Water and extremophile microbiome

Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms
Weil T. – Microbiome

Built environment

Bacterial diversity on rock surface of the ruined part of a French historic monument: The Chaalis abbey
Agnes Mihajlovski – International Biodeterioration & Biodegradation

Food microbiology

Diversity of the dominant bacterial species on sliced cooked pork products at expiration date in the Belgian retail
Wim Geeraerts – Food Microbiology


Agar-degrading bacteria isolated from Antarctic macroalgae – Folia Microbiologica
Roxana Alvarado & Sergio Leiva

Exploring the Antimicrobial and Antitumor Potentials of Streptomyces sp. AGM12-1 Isolated from Egyptian Soil
Maged S. Ahmad – Frontiers in Microbiology

Phages and viruses

Review: Virus–host interactions and their roles in coral reef health and disease
Rebecca Vega Thurber – Nature Reviews Microbiology

Review: Mimivirus: leading the way in the discovery of giant viruses of amoebae
Phillippe Colson – Nature Reviews Microbiology

Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment
Highfield A. – Viruses

Techniques and methods

Review: Current state and applications of microbial genome‐scale metabolic models
Won Jun Kim – Current Opinion in Systems Biology

A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens
Lee S. Katz – Frontiers in Microbiology

FurIOS: A Web-Based Tool for Identification of Vibrionaceae Species Using the fur Gene
Henrique Machado – Frontiers in Microbiology

Research Highlights (a few from today’s issue of Nature Reviews Microbiology):

Bacterial Physiology: Treadmilling runs bacterial division – Ashley York

Symbiosis: Wolbachia’s matchmaking secret revealed – Ursula Hofer

Bacterial Physiology: Persisters running out of energy – Andrea Du Toit

Bacterial pathogenesis: Hitching a ride with DCs – Yvonne Bordon

Microbes in the news

Light rain can spread soil bacteria far and wide, study finds
Science Daily – Paper by Young Soo Joung available here.

Novel antibiotic combination therapy overcomes deadly drug-resistant bacteria
Case Western Reserve University – EurekAlert!

Researchers track spread of multidrug-resistant bacteria in hospital sinks
University of Virginia – Paper by Kotay S. available here.

Microbes on the market

CRISPR patent results
Shimona Starling – Nature Reviews Microbiology

Global Microbiology Testing Market Present Scenario and Growth Prospects 2016-2021

March 3, 2017

Our post today has been remodeled after some small technical problems, but here’s your fresh Friday digest of microbiome papers!

Events and jobs

Full-time visiting faculty position in biochemistry and microbiology (2017-18)
College of the Holy Cross – Worcester, Massachussets

Microbiology Laboratory Technician
Symbio Laboratories – Brisbane, Australia

Team Manager – Microbiology
AstraZeneca – Cambridge, UK

27th European Congress of Clinical Microbiology & Infectious Diseases
Vienna – Austria

General microbiome

Cryptic biogeochemical cycles: unravelling hidden redox reactions
Andreas Kappler – Environmental Microbiology

Multi-site human microbiome

Microbe-microbe and host-microbe interactions drive microbiome dysbiosis and inflammatory processes
AD Proal – Discovery Medicine

The human microbiome: an emerging tool in forensics
Jarrad T. Hampton-Marcell – Microbial Biotechnology

The salivary microbiome is altered in the presence of a high salivary glucose concentration
J. Max Goodson – Plos One

Human vaginal microbiome

Review: The role of Escherichia coli in reproductive health: state of the art.
P. Cools – Research in Microbiology

Survival of vaginal microorganisms in three commercially available transport systems.
Allison L DeMarco – Anaerobe

Human gut microbiome

Small Intestinal Bacterial Overgrowth Is Associated with Non-Alcoholic Fatty Liver Disease.
A. Fialho – Journal of Gastrointestinal and Liver Disease

Review: Roles of the intestinal microbiota in pathogen protection.
C. Ubeda – Clinical Translational Immunology

Atopic dermatitis and gut microbiota
M. Lindberg – British Journal of Dermatology

Editorial: The gut microbiota and psychiatric illness
Glenda MacQueen – Journal of Psychiatry and Neuroscience

Commentary: For Health Disparities, Don’t Ignore the Microbiome
Jennifer Abbasi – JAMA

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

Multi-Omics Reveals that Lead Exposure Disturbs Gut Microbiome Development, Key Metabolites and Metabolic Pathways
Bei Gao – Chemical Research in Toxicology

Animal experiments

Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice.
Giada de Palma – Science Translational Medicine

Targeting the Microbiota-Gut-Brain Axis: Prebiotics Have Anxiolytic and Antidepressant-like Effects and Reverse the Impact of Chronic Stress in Mice
Aurelijus Burokas – Biological Psychiatry

Animal microbiome

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
Mathieu Groussin – Nature Communications

Transition of the intestinal microbiota of dogs with age.
H. Masuoka – Biosciences Microbiota Food Health

Comparative analysis of gut microbiota of mosquito communities in central Illinois.
EJ Muturi – PLoS Neglected Tropical Diseases

Transformation, Proliferation, and Influence on Host Performance by Three Gut Bacteria in the Rice Water Weevil (Coleoptera: Curculionidae)
Yunshan Huang – Annals of the Entomological Society of America

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island
Jan M. Meyer – Environmental Microbiology

MALDI-TOF MS identification of microbiota associated with pest insect Diabrotica speciosa
Bruno Perlatti – Agricultural and Forest Entomology

Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria
Alyce Taylor-Brown – Environmental Microbiology

Plant, root, and soil microbiome

Syntrophobacteraceae-affiliated species are major propionate-degrading sulfate reducers in paddy soil
Pengfei Liu – Environmental Microbiology

Next-Generation Sequencing Analyses of Bacterial Community Structures in Soybean Pastes Produced in Northeast China
Mi-Hwa Lee – Journal of Food Science

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

Water and extremophile microbiome

Metagenomic analysis reveals unusually high incidence of proteorhodopsin genes in the ultraoligotrophic Eastern Mediterranean Sea
Vadim Dubinsky – Environmental Microbiology

Bacterial activity in hydrogenetic ferromanganese crust from the Indian Ocean: a combined geochemical, experimental and pyrosequencing study
PP Sujith – Environmental Earth Sciences

Stoichiometry of Prochlorococcus, Synechococcus, and small eukaryotic populations in the western North Atlantic Ocean
Steven E. Baer – Environmental Microbiology

Built environment

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

Spread from the Sink to the Patient: in situ Study Using Green Fluorescent Protein (GFP) Expressing- Escherichia coli to Model Bacterial Dispersion from Hand Washing Sink Trap Reservoirs
Shireen Kotay – Applied and Environmental Microbiology

Phages and viruses

Pre-print: How to name and classify your phage: an informal guide
Evelien M. Adriaenssens – bioRxiv

Review: Tumor-associated macrophages: implications in cancer immunotherapy
Amy J Petty – Immunotherapy

Predation by Bdellovibrio bacteriovorus significantly reduces viability and alters the microbial community composition of activated sludge flocs and granules
Shugeng Feng – FEMS Microbiology Ecology


The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis
Sylwia Zielinska – MicrobiologyOpen

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
Jason L. Weirather – F1000 Open Research

A High-Throughput Screening Platform of Microbial Natural Products for the Discovery of Molecules with Antibiofilm Properties against Salmonella
Sonia Paytubi – Frontiers in Microbiology

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data
Mohamed Mysara – GigaDB


Highlights: Evolving as a holobiont
Lauren A. Richardson – Plos Biology

Microbes in the news

Gut microbes and poor artery health – researchers probe possible link
Jim Scott – CU Boulder Today

February 19, 2017.

A light digest for today’s Sunday morning. A variety of human microbiome papers and a review on the evolution of antimicrobial resistance.

Human respiratory microbiome

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients. Poala J Marino. Journal of Critical Care.

Human nearly-sterile sites

Short communication: Epicardial Adipose Tissue Microbial Colonization and Inflammasome Activation in Acute Coronary Syndrome. Daniela Pedicino. International Journal of Cardiology.

Human gut microbiome

Microbiota Disruption Induced by Early Use of Broad Spectrum Antibiotics is an Independent Risk Factor of Outcome after Allogeneic Stem Cell Transplantation. Daniela Weber.
Biology of Blood and Marrow Transplantation.

Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept. Vera Slomka. Clinical Periodontology.

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota. A. Sloan Devlin. Cell Host & Microbe.

Animal experiments

Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes. Julia H. Kreznar. Cell Reports.

Microbes in the environment

Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds. M Herrmann. Microbial Ecology.

Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats. Adriano Cabal. Microbiology Open.

Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa. Relebohile Matthew Matobole. Marine Drugs.

Food microbiology

Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods. Luana Martins Perin. Food Microbiology.

Perspective: New insights on the use of wine yeasts. Francesca Comitini. Current Opinion in Food Science.

Phages and viruses

Pre-print: Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments. Samuel L. Díaz Muñoz. bioRxiv.


Virulence Inhibitors from Brazilian Peppertree Block Quorum Sensing and Abate Dermonecrosis in Skin Infection Models. Amelia Muhs. Scientific Reports.


Review: Epistasis and the Evolution of Antimicrobial Resistance. Alex Wong. Frontiers Microbiology.