March 27, 2017

Exploring life within the biofilm and how free-living microbes thrive, and focus on life history patterns of symbionts. Finally, big dairy (Parmalat- South Africa)  was found guilty of repeatedly hiding serious infections (Salmonella and Listeria,)from their consumers.

General microbiome

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions.

Wang D. ISME Journal

Symbiont Acquisition and Replacement as a Source of Ecological Innovation.

Sudakaran S. Trends in Microbiology

Distinct succession patterns of abundant and rare bacteria in temporal microcosms with pollutants.

Jiao S. Environmental Pollution

Similar articles

Human gut microbiome

Early-life origin of intestinal inflammatory disorders.

Ley D. Nutrition Reviews

From mystery to mechanism: Can proteomics build systems-level understanding of our gut microbes?

Gonzalez CG. Expert Reviews of Proteomics

Human oral microbiome

Circadian oscillations of microbial and functional composition in the human salivary microbiome.

Takayasu L. DNA Research

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.

Yamagishi J.PLoS One.

Water, estuarine and marine microbiome

Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics.

Moitinho-Silva L. ISME Journal

Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes.

Berry MA. Frontiers in Microbiology

Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens.

Mohiuddin MM. Water Research

Symbiosis and microbiome flexibility in calcifying benthic foraminifera of the Great Barrier Reef.

Prazeres M. Microbiome

Farm animal microbiome

Effects of dietary rapeseed meal supplementation on cecal microbiota in laying hens with different flavin-containing monooxygenase 3 genotypes.

Long C. Poultry Science

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot.

Maboni G. Scientific Reports

Pasture flock chicken cecal microbiome responses to prebiotics and plum fiber feed amendments.

Park SH. Poultry Science

Respiratory system microbiome

Dendritic cell expression of the signaling molecule TRAF6 is required for immune tolerance in the lung.

Han D. International Immunology

Eukaryote microbiome

UniEuk: Time to Speak a Common Language in Protistology!

Berney C. The Journal of Eukaryotic Microbiology

Animal microbiome

Colonization by non-pathogenic bacteria alters mRNA expression of cytochromes P450 in originally germ-free mice.

Jourová L. Folia Microbiologica

Gut microbiome-related metabolic changes in plasma of antibiotic-treated rats.

Behr C. Archives of Toxicology

Indoor microbiome

Hospital microbial surface colonization revealed during monitoring of Klebsiella spp., Pseudomonas aeruginosa, and non-tuberculous mycobacteria.

Geadas Farias P. Antonie Van Leeuwenhoek

Microbes in the news

Parmalat hides bacteria infections


Indians find a new bacterial target for drug development

-The Hindu

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

Microbiome stock photo fails

Sometimes I come across a stock photo that is unintentionally funny. Here is another one.

An artist’s rendition of how microbes grow in the intestinal tract. Here you can see bacteria circling around microvilli. Or are they shiny pills in straight lines circling around sausages, or decaying fingers in plastic gloves?

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Screen Shot 2017-03-23 at 9.30.48 PM.pngScreen Shot 2017-03-23 at 9.29.47 PM

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Same villi but different bacteria. It’s a Fecal Microbiota Transplant!


And this one has no bacteria at all. I guess it represents the Germ Free Mouse.


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 19, 2017

A nice collection of articles this Sunday. We look at the potential benefits of Fecal Microbiota Transplantation,  a number of probiotic articles, and microbiota manipulations in animals. 


Events and jobs

Pharmaceutical Microbiology Laboratory Manager – Derbyshire / Edinburgh

General microbiome

Role of the small intestine, colon and microbiota in determining the metabolic fate of polyphenols – Gary Williamson – Biochemical Pharmacology

Fecal microbiota transplantation (FMT) could reverse the severity of experimental necrotizing enterocolitis (NEC) via oxidative stress modulation – Xiaomei Li –

Free Radical Biology and Medicine

PREPRINT: Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics – Ashish A Malik – BioRxiv

Human respiratory microbiome

Review: Normal Oral Flora and the Oral Ecosystem – Lakshman Samaranayake – Dental Clinics of North America

Oral Bacterial Infections : Diagnosis and Management – Glendee Reynolds-Campbell – Dental Clinics of North America

Human gut microbiome 

The gut microbiota metabolism of pomegranate or walnut ellagitannins yields two urolithin-metabotypes that correlate with cardiometabolic risk biomarkers: comparison between normoweight, overweight-obesity and metabolic syndrome – María V. Selma – Clinical Nutrition

Animal experiments

Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout – David Huyben –


Host Intestinal Epithelium Derived Mirnas Shape The Microbiota And Its Implication In Cardiovascular Diseases – Lianbi Zhao – Journal of the American College of Cardiology

The effect of penicillin administration in early life on murine gut microbiota and blood lymphocyte subsets – Jaroslaw Daniluk – Anaerobe

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

Animal microbiomes

Hunting for healthy microbiomes: determining the core microbiomes of Ceratina, Megalopta, and Apis bees and how they associate with microbes in bee collected pollen – Peter Graystock – Conservation Genetics

Water and extremophile microbiome  

Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages – Takumi Murakami – Microbes and Environments

Food microbiology

Biopreservation potential of lactic acid bacteria from Andean fermented food of vegetal origin – Alba Yépez – Food Control

Metaproteomic analysis of microbiota in the fermented fish, Siniperca chuatsi – Chaofan Ji – LWT – Food Science and Technology

Probiotics / prebiotics 

The use of potential probiotic Lactobacillus plantarum DW12 for producing a novel functional beverage from mature coconut water – Duangporn Kantachote – Journal of Functional Foods

Autochthonous lactic acid bacteria with probiotic aptitudes as starter cultures for fish-based products – Barbara Speranza – Food Microbiology

Functional probiotic products based on fermented buckwheat with Lactobacillus rhamnosus – Zuzana Matejčeková – LWT – Food Science and Technology


Organism and Microbiome Analysis: Techniques and Implications for Chronic Rhinosinusitis – Ashleigh A. Halderman – Otolaryngologic Clinics of North America

Microbes in the news

Vitamin May be Key to Killing Cancer-Causing Bacteria Carole Ellis ContagionLive

Changes in gut microbiota after unhealthy diet may protect from metabolic disease – Medical Press

Porridge really is that good for you – The Independent

Antibiotics and the honeybee microbiome – Kerry Evans – Labroots

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 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