April 28, 2017

Quite a few interesting articles and news about microbes: are we colonised with bacteria in utero? What is the relevance of cooperative interactions in microbial biotechnological processes? Microbe colonies  in space? Read more in today’s Microbiome Digest..

General microbiome

Variable habitat conditions drive species covariation in the human microbiota – Charles K. Fisher – PLOS

Pregnancy and early life

*Review: The prenatal gut microbiome: are we colonized with bacteria in utero? – R. W. Walker – Pediatric Obesity

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study – Mohan Pammi – PLOS
 Human respiratory microbiome

A commensal streptococcus hijacks a Pseudomonas aeruginosa exopolysaccharide to promote biofilm formation – Jessica A. Scoffield – PLOS
Human oral microbiome

A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis – Matthias Munz – Human Molecular Genetics

Human nearly-sterile sites 

A case of polymicrobial anaerobic spondylodiscitis due to Parvimonas micra and Fusobacterium nucleatum – Leanne M Cleaver – JMM Case Reports

Human gut microbiome

Small Molecules from Deep within the Gut – Michael Ehrmann – ChemBioChem

Single Delivery of High-Diversity Fecal Microbiota Preparation by Colonoscopy Is Safe and Effective in Increasing Microbial Diversity in Active Ulcerative Colitis – Jacob Vinita – Inflammatory Bowel Diseases

Fecal Microbiota Transplantation for Refractory Clostridium difficile Colitis in Solid Organ Transplant Recipients – R. J. Friedman-Moraco – American Journal of Transplantation

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses – Konstantin Yarygin – PLOS
Animal experiments

Neonatal mono-colonization of germ-free mice with Lactobacillus casei enhances casein immunogenicity after oral sensitization to cow’s milk – Matieny Aicha Maiga – Molecular Nutrition & Food Research

Shifts in the Gut Microbiota Composition Due to Depleted Bone Marrow Beta Adrenergic Signaling Are Associated with Suppressed Inflammatory Transcriptional Networks in the Mouse Colon – Tao Yang – Frontiers in Physiology

Animal microbiome

Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population – Nádia Conceição-Neto – Ecology and Evolution

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders – C Karlsen – Journal of Fish Diseases

Plant, root, and soil microbiome

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content – Pankaj Trivedi – Environmental Microbiology

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco) – Odile Bruneel –  Extremophiles

Water and extremophile microbiome 

Geochemistry and microbial diversity of cave waters in the gypsum karst aquifers of Emilia Romagna region, Italy – Ilenia M. D’Angeli – Science of The Total Environment
Probiotics / prebiotics

Characterization, identification and application of lactic acid bacteria isolated from Leymus chinensis silage – Qing Zhang – Grassland Science

*Review: Cooperation in microbial communities and their biotechnological applications – Matteo Cavaliere – Environmental Microbiology


MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data – Achal Dhariwal – Nucleic Acid Research

Microbes in the news

Adaptive Phage Therapeutics – Terminally Ill Patient Successfully Treated With Bacteriophage – BioSpace

Research Links Microbiome Makeup To Remission in Pediatric Crohn’s – Gastroenterology & Endoscopy News

NASA Astronauts Are Close to Identifying Unknown Microbe Colonies That Grow in Space – Sciencealert.com


April 27, 2017

An exploration of fish as an alternative to mice for models of host-microbe interactions, a review on what we can learn from Bacteroides about the gut micriobiome, a news story on successful phage therapy for a multi drug resistant infection.

Human oral microbiome

The human oral microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely-related individuals – Liam Shaw – bioRxiv

Human gut microbiome

* Review: An insider’s perspective: Bacteroides as a window into the microbiome – Aaron G Wexler – Nature Microbiology

Gut Microbiota: Small Molecules Modulate Host Cellular Functions – Jacob M. Luber – Current Biology

Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis – Tzipi Braun – Scientific Reports

Animal experiments

Supplemental feeding of a gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, alleviates spontaneous atopic dermatitis and modulates intestinal microbiota in NC/nga mice – Hiroko Kaikiri – International Journal of Food Sciences and Nutrition

Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation – Chris Flemming – Microbiome

Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction – Shiran Gerassy-Vainberg – Gut

Animal microbiome

Tick-Pathogen Interactions and Vector Competence: Identification of Molecular Drivers for Tick-Borne Diseases – José de la Fuente – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Review: Managing the plant microbiome for biocontrol fungi: examples from Hypocreales – Ryan M Kepler – Current Opinion in Microbiology

Occurrence of perchlorate in groundwater, paired farmland soil, lettuce, and rhizosphere soil from Chengdu, China – Yulu Tang – Environmental Science: Processes & Impact

Water and extremophile microbiome

The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions – Michael D Lee – The ISME Journal

Bringing methanotrophy in rivers out of the shadows – Felicity Shelley – Limnology and Oceanography

Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community – Andrea Di Cesare – Environmental Pollution

Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production – R Kanniah Goud – Bioresource Technology


Perspective: Next-generation probiotics: the spectrum from probiotics to live biotherapeutics – Paul W O’Toole – Nature Microbiology

Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ


Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments – Arghya Mukherjee – Scientific Reports


Faecal volatile organic compounds analysis using field asymmetric ion mobility spectrometry: non-invasive diagnostics in paediatric inflammatory bowel disease – Nora van Gaal – Journal of Breath Research

Teleosts as Model Organisms to Understand Host-Microbe Interactions – Emily A Lescak – Journal of Bacteriology

Synthetic and analytical strategies for the quantification of phenyl-γ-valerolactone conjugated metabolites in human urine – Nicoletta Brindani – Molecular Nutrition & Food Research

More microbes

Species ecological similarity modulates the importance of colonization history for adaptive radiation – Jiaqi Tan – International Journal of Organic Evolution

Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells – Yosuke Tashiro – Frontiers in Microbiology

Microbes in the news

Phage Therapy Saves Patient from Drug-Resistant Microbes – Genetic Engineering & Biotechnology News

Chronic fatigue syndrome linked to imbalanced microbiome – EurekAlert

Komodo Dragon Blood Could Become Tool in Fight Against Bacteria – Elizabeth Pratt – Healthline

Researchers move closer to preventing frost damage in vineyards by managing bacteria on the vines – Greg Northcutt – Western FarmPress

Underwater volcano eruptions allow new bacteria to take over seafloor – Lisa-Ann Lee – New Atlas

Microbes on the market

Taconic Biosciences Expands Microbiome Product and Service Platform – GlobeNewswire

Bacteria and art

This Art Exhibition Is Made From Bacteria, Live Insects And Human Sweat – Ryan F Mandelbaum – Gizmodo Australia

Art Made with CRISPR Aims to Raise Awareness of Antibiotic Resistance – Clara Rodríguez Fernández – Labiotech.eu

Amy’s non-microbiology picks

Microscopy: A larger palette for biological imaging – Charles H Camp Jr – Nature

April 26, 2017

A series of commentary on the effects of microbiota on vaccines, a fascinating news release about a phage therapy against multi-drug resistant bacterial infection, and can our gut microbes tell us what to eat?

General microbiology

Evaluation of serotypes 5 and 8 capsular polysaccharides in protection against Staphylococcus aureus in murine models of infection – Brian L. Cheng – Human Vaccines & Immunotherapeutics

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? If So, Is There Potential for Efficacious Microbiota-Based Vaccines? – Dan R Littman – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Engaging Our Endogenous Adjuvants – Nicholas Collins1 and Yasmine Belkaid – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Issues of Sovereignty, Federalism, and Points-Testing in the Prokaryotic and Eukaryotic Spaces of the Host-Microbial Superorganism – Andrew J. Macpherson – Cold Spring Harbor Perspectives in Biology

Web alert: Microbial therapeutics – Microbial Biotechnology

Human multi-site microbiome

The urinary microbiome and its contribution to lower urinary tract symptoms; ICI-RS 2015 – Marcus J. Drake – Neurourology and Urodynamics

Human gut microbiome

Doctoral Dissertation: The Effects of the Gut Microbiota on the Host Chromatin Landscape – Nicholas Paul Semenkovich – University of Washington, St. Louis

Tissue adaptation: Implications for gut immunity and tolerance – Ana M.C. Faria – Journal of Experimental Medicine

Animal experiments

Doctoral Dissertation, Mouse: The impact of malnutrition on host-microbe interactions in the intestine – Eric Brown – University of British Columbia

Mouse: Deciphering the mechanism of Huang-Lian-Jie-Du-Decoction on the treatment of sepsis by formula decomposition and metabolomics: enhancement of cholinergic pathways and inhibition of HMGB-1/TLR4/NF-κB signaling – Dingqiao Xu – Pharmacological Research

Dysbiosis of intestinal microbiota and decrease in paneth cell antimicrobial peptide level during acute necrotizing pancreatitis in rats – Jing Chen – PLoS One

Commensal bacteria and essential amino acids control food choice behavior and reproduction – Ricardo Leitão-Gonçalves – PLoS Biology

Press: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh – Scientific American

Press: Are Gut Bacteria Driving Your Cravings? – Shayla Love – Vice

Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice – Annadora J. Bruce-Keller – PLoS One

Animal microbiome

Discovery of tauroursodeoxycholic acid biotransformation enzymes from the gut microbiome of black bears using metagenomics – Can Song – Scientific Reports

Diversity and functions of the sheep faecal microbiota: a multi-omic characterization – Alessandro Tanca – Microbial Biotechnology

New issue of Microbial Biotechnology is available online.

Plant, root and soil microbiome

Microbial communities associated with plants: learning from nature to apply it in agriculture – Fernando Dini Andreote and Michele de Cássia Pereira e Silva- Current Opinion in Microbiology

Life in earth – the root microbiome to the rescue? – Tim H Mauchline, Jacob G Malone – Current Opinion in Microbiology

Unique rhizosphere micro-characteristics facilitate phytoextraction of multiple metals in soil by the hyperaccumulating plant Sedum alfredii – Dandi Hou – Environmental Science & Technology

Water and extremophile microbiome

Doctoral Dissertation: Microbial community variation in an Arctic shelf seafloor – Tan Thi Nguyen – The Arctic University of Norway

Diversity Analysis and Bioresource Characterization of Halophilic Bacteria Isolated from a South African Saltpan – Ramganesh Selvarajan – Molecules

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis – Daniel Kurth – Scientific Reports


VSL#3 probiotic differently influences IEC-6 intestinal epithelial cell status and function – Benedetta Cinque – Journal of Cellular Physiology

Phages and viruses

Press Release: Novel phage therapy saves patient with multidrug-resistant bacterial infection – University of California, San Diego


Preprint: Assessing species biomass contributions in microbial communities via metaproteomics – Manuel Kleiner – bioRxiv

Microbes in the news

Are Probiotics the Answer to Acne? – Kristen Fischer – Healthline News

Are the microbes in our gut affecting how fast we age? – Vincent Maffei – OUPblog

Bacteria May be Reason Some Foods Cause Heart Disease, Stroke – Maggie Fox – NBC News

The Slow-Motion Bacteria Buried Deep in the Ocean’s Floor – Veronique Greenwood – The Atlantic

Bacteria from India’s hot springs could help contain oil spills – Dinesh C Sharma – Firstpost

Bacteria causing diarrhoea deaths in children resists key antibiotic – Syed Akbar – The Times of India

Fat rats, slow sperm, and unhealthy bacteria – Lee Evslin – The Garden Island

April 25, 2017

A bit of a late morning Digest today, as it is packed with articles! Diverse themes, such as rhizosphere microbiome, lots of biotechnology pieces, and insightful reviews on gut microbiota and herbivory, “wild” microbiomes and ecological stoichiometry.

General microbiome

Review: The microbiome in anti-cancer therapy
Stavros Bashiardes et al – Seminars in Immunology

Perspective: Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk
Marco Romano – Frontiers in Microbiology

Multi-site human microbiome

Review: Lung Homeostasis: Influence of Age, Microbes, and the Immune System
Clare M. Lloyd & Benjamin J. Marsland – Immunity

Human epitelial microbiome

The oral microbiome community variations associated with normal, potentially malignant disorders and malignant lesions of the oral cavity
Mok Shao Feng et al – Malaysian Journal of Pathology

Human gut microbiome

‘Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance
Rankin A. et al – Journal of Sports Medicine

Effect of pistachio consumption on the modulation of urinary gut microbiota-related metabolites in prediabetic subjects
Hernandéz-Alonso P et al – Journal of Nutritional Biochemistry

Microbial diseases

Alteration of stomach microbiota compositions in the progression of gastritis induces nitric oxide in gastric cell
Tianyi Dong et al – Experimental and Therapeutic Medicine

General environmental microbiome

Review: Evolutionary Biology Needs Wild Microbiomes
Sarah M. Hird – Frontiers in Microbiology

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites
Diego M. Toneatti et al – Frontiers in Microbiology

Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms
Daniella Gat et al – Environmental Science and Technology

Animal experiments

Urinary and Fecal Metabonomics Study of the Protective Effect of Chaihu-Shu-Gan-San on Antibiotic Induced Gut Microbiota Dysbiosis in Rats
Meng Yu et al – Nature Scientific Reports

Proteomic analysis of a mosquito host cell response to persistent Wolbachia infection
Gerald Baldridge et al – Research in Microbiology

Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers
Yan Li et al – BMC Microbiology

Effects of various weaning times on growth performance, rumen fermentation and microbial population of yellow cattle calves
Mao H et al – Asian-Australasian Journal of Animal Science

Effects of various levels of dietary copper supplementation with copper sulfate and copper hydroxychloride on Pacific white shrimp Litopenaeus vannamei performance and microbial communities
Yangen Zhou et al – Aquaculture

Plant, root, and soil microbiome

Soil Acidification Aggravates the Occurrence of Bacterial Wilt in South China
Shili Li et al – Frontiers in Microbiology

Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato
Mélanie M. Paulin et al – Applied and Environmental Microbiology

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil
Yang W et al – Environmental Science and Pollution Research

Rhizosphere Engineering: Enhancing Sustainable Plant Ecosystem Productivity in a Challenging Climate
Amirhossein Ahkami et al – Rhizosphere

Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies
Feigl V et al – Science of the Total Environment

Response of microbial community of organic-matter-impoverished arable soil to long-term application of soil conditioner derived from dynamic rapid fermentation of food waste
Jiaqi Hou et al – Plos One

Effects of adding trace elements on rice straw anaerobic mono-digestion: Focus on changes in microbial communities using high-throughput sequencing
Yafan Cai et al – Bioresource Technology

Cereal-legume intercropping modifies the dynamics of the active rhizospheric bacterial community
E. Taschen et al – Rhizosphere

Water, estuarine and sediment microbiome

Microbial Community Response on Wastewater Discharge in Boreal Lake Sediments
Jatta Saarenheimo et al – Frontiers in Microbiology

Perspective: The Hadal Biosphere: Recent insights and new directions
Rulong Liu et al – Deep Sea Research Part II: Topical Studies in Oceanography

Bacterial community dynamics and functional variation during the long-term decomposition of cyanobacterial blooms in-vitro
Limei Shi et al – Science of the Total Environment

Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean
Julie Dinasquet et al – Environmental Microbiology

DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom
Christian Wurzbacher et al – Environmental Microbiology Reports

Shifts in soil microbial metabolic activities and community structures along a salinity gradient of irrigation water in a typical arid region of China
Lijuan Chen et al – Science of the Total Environment

Large-scale seaweed cultivation diverges water and sediment microbial communities in the coast of Nan’ao Island, South China Sea
Xinfei Xie et al – Science of The Total Environment

Extremophile and space microbiome

Review: Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth
Fathi Karouia – Biotechnology Advances

Built environment

Diversity changes of microbial communities into hospital surface environments
Rika Yano et al – Journal of Infection and Chemotherapy

Microbial communities in the functional areas of a biofilm reactor with anaerobic-aerobic process for oily wastewater treatment
Li J et al – Bioresource Technology

Dominance of candidate Saccharibacteria in a membrane bioreactor treating medium age landfill leachate: Effects of organic load on microbial communities, hydrolytic potential and extracellular polymeric substances
Remmas N. et al – Bioresource Technology

Microbial biotechnology

Review: Uncovering Potential Applications of Cyanobacteria and Algal Metabolites in Biology, Agriculture and Medicine: Current Status and Future Prospects
Rachana Singh et al – Frontiers in Microbiology

The Ability of Typha angustifolia L. for Degradation of BOD and COD in Wastewater of Tofu Industry Using Phytoremediation
Pertiwi Andarani et al – Advanced Science Letters

Reversible Anaerob-Evapotranspiration Process for Removal of High Strength Ammonium in Leachate from Tropical Landfill
Badrus Zaman et al – Advanced Science Letters

Strain specific variation in plant growth promoting volatile organic compound production by five different Pseudomonas spp. as confirmed by response of Vigna radiata seedlings
Jishma P et al – Journal of Applied Microbiology

Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture
Zhao S. et al – Applied Microbiology and Biotechnology

Inhibitory effect of coumarin on syntrophic fatty acid oxidizing and methanogenic cultures and biogas reactor microbiomes
Denny Popp et al – Applied and Environmental Microbiology

Food microbiology

Impact of solar radiation exposure on phyllosphere bacterial community of red-pigmented baby leaf lettuce
Pilar Truchado et al – Food Microbiology

Effect of abattoir and cut on variations in microbial communities of vacuum-packaged beef
Mandeep Kaur et al – Meat Science

Smokeless tobacco products harbor diverse bacterial microbiota that differ across products and brands
Smyth EM et al – Applied Microbiology and Biotechnology
General Microbiology

Protein Acetylation and Its Role in Bacterial Virulence
Jie Ren et al – Trends in Microbiology

Perspective: Ecological Stoichiometry beyond Redfield: An Ionomic Perspective on Elemental Homeostasis
Punidan D. Jeyasingh et al – Frontiers in Microbiology


Complete Genome Sequence of Pseudomonas protegens H78, a Plant Growth–Promoting Rhizobacterium
Xianqing Huang et al – Genome Announcements

Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria, Carboxydocella sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic Fronts in Japan
Yuto Fukuyama et al – Genome Announcements

The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Ana Gutiérrez-Preciado et al – PeerJ

Phages and viruses

A novel type of polyhedral viruses infecting hyperthermophilic archaea
Ying Liu et al – Journal of Virology

Phage therapy: an alternative or adjunct to antibiotics?
Shawna McCallin & Harald Brüssow – Emerging Topics in Life Sciences

Highlights from the HIV Research for Prevention Conference (R4P)
Sandhya Vasan et al – Journal of Virus Eradication

Bioinformatics and statistics

A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping
Hyunwook Koh et al – Microbiome

The BRENDA Enzyme Information System–From a Database to an Expert System
I. Schomburg et al – Journal of Biotechnology

HirBin: high-resolution identification of differentially abundant functions in metagenomes
Tobias Österlund et al – BMC Genomics

A novel genome signature based on inter-nucleotide distances profiles for visualization of metagenomic data
Xian-Hua Xie et al – Physica A: Statistical Mechanics and its Applications

Data Intensive Genome Level Analysis for Identifying Novel,Non-Toxic Drug Targets for Multi Drug Resistant Mycobacterium tuberculosis
Divneet Kaur et al – Nature Scientific Reports

Techniques and methods

Building a Translational Microbiome Toolbox
Payal Joglekar & Julia Segre – Cell

April 24, 2017

General Microbiome

Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology

Dietary High Zinc Oxide Modulates the Microbiome of Ileum and Colon in Weaned Piglets – Ting Yu – Frontiers in Microbiology

Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments –  Matthew L Jenior – BioRxiv

Review: Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies – Kequan Zhou – Journal of Functional Foods

Protective effects of milk fermented by Lactobacillus plantarum B7 from Brazilian artisanal cheese on a Salmonella enterica serovar Typhimurium infection in BALB/c mice – Journal of Functional Foods



Molecular Demonstration of a Pneumocystis Outbreak in Stem Cell Transplant Patients: Evidence for Transmission in the Daycare Center – Frontiers in Microbiology

A New Rabbit-skin Model to Evaluate Protective Efficacy of Tuberculosis Vaccines – Xun Liu – Frontiers in Microbiology

Molecular epidemiology and antibiotic resistance profiles of methicillin-resistant Staphylococcus aureus strains in a tertiary hospital in China – Haishen Kong – Frontiers in Microbiology


Environmental Microbiology

Microbial community assembly differs by mineral type in the rhizosphere – Thea Whitman – BioRxiv

Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato – Applied Environmental Microbiology

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean – Tom O. Delmont – BioRxiv

Bacterial communities in boreal forest mushrooms are shaped both by soil parameters and host identity – Mari Pent – Frontiers in Microbiology



Isoprenoid Pyrophosphate-Dependent Transcriptional Regulation of Carotenogenesis in Corynebacterium glutamicum – Nadja A. Henke – Frontiers in Microbiology

Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements – Xavier Argemi – Genome Biology and Evolution

Pooled CRISPR interference screens enable high-throughput functional genomics study and elucidate new rules for guide RNA library design in Escherichia coli – Tianmin Wang – BioRxiv



Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution –  Joanna M. Wolfe – BioRxiv



AliTV-interactive visualization of whole genome comparisons – Markus J. Ankenbrand – PeerJ (not peer-reviewed)

TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation – Ali Z Ijaz – PeerJ (not peer-reviewed)



Preprinting Microbiology – Patrick D Schloss – BioRxiv


Non – Microbiology picks

News: Scientists across the world take to the streets to demand freedom from political interference – The Telegraph (via Yahoo News)

Human umbilical cord plasma proteins revitalize hippocampal function in aged mice – Joseph M. Castellano –  Nature


April 23, 2017

Water and extremophile microbiome

Size fractionated phytoplankton biomass and net metabolism along a tropical estuarine gradient – Sara Soria-Píriz – Limnology and Oceanography

Tropical mangrove swamp metagenome reveals unusual abundance of ecologically important microbes – Zahidah Ismail – Current Science


HirBin: high-resolution identification of differentially abundant functions in metagenomes – Tobias Österlund – BMC Genomics

Microbes in the news

Using elements of viruses, antibodies to fight resistant bacteria – Chris Dall – CIDRAP News

Lower Hutt officials investigate bacteria in water – Newshub

Stowaway Bacteria Could Be Even More Contagious in Space Than We Thought – Peter Dockrill – Science Alert

April 22, 2017

General microbiome

The Microbiome – The Biochemist (full issue)

Human vaginal microbiome

*Review: What fertility specialists should know about the vaginal microbiome: a review – Juan Antonio García-Velascoa – Reproductive BioMedicine Online

Animal experiments

Microbiota-Induced Antibodies Are Essential for Host Inflammatory Responsiveness to Sterile and Infectious Stimuli – Daniel Cisalpino – Journal of Immunology

Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans – Timothy A. Scott – Cell

Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics – Aurian P. García-González – Cell

Examining the role of the microbiome in the effectiveness of colorectal cancer treatment – Jim Fessenden – UMass Medical School Communications

Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens – Yun-Gi Kim – Science

Infant mice lack microbes that help fight intestinal infection – EurekAlert!

Effects of different oligosaccharides at various dosages on the composition of gut microbiota and short-chain fatty acids in mice with constipation – Linlin Wang –  Food & Function

Short Term High Fat Diet Induces Obesity-Enhancing Changes in Mouse Gut Microbiota That are Partially Reversed by Cessation of the High Fat Diet – Yue Shang – Lipids

Animal microbiome

Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature – Andrian P. Gajigan – Microbiology Open

Characterization of the gut microbiota in the golden takin (Budorcas taxicolor bedfordi) – Jun Chen – AMB Express

*Opinion: Mammary microbiota of dairy ruminants: fact or fiction? – Pascal Rainard – Veterinary Research

Determination of the microbial community features of Haemaphysalis flava in different developmental stages by high-throughput sequencing – Deyong Duan – Journal of Basic Microbiology

Plant, root, and soil microbiome

A signature of tree health? Shifts in the microbiome and the ecological drivers of horse chestnut bleeding canker disease – Britt Koskella – New Phytologist

Soil aggregates as massively concurrent evolutionary incubators – Matthias C Rillig – ISME

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment – Qing Wang – Biology and Fertility of Soils

*Editorial: Signalling in the phytomicrobiome: Understanding and harnessing the plant holobiont – Donald L. Smith – Frontiers in Plant Science

Warming enhances old organic carbon decomposition through altering functional microbial communities – Lei Cheng – ISME

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Long-term straw returning affects Nitrospira-like nitrite oxidizing bacterial community in a rapeseed-rice rotation soil – Xuesong Luo – Journal of Basic Microbiology

Water and extremophile microbiome

Attenuation and modification of the ballast water microbial community during voyages into the Canadian Arctic – Mattias L. Johansson – Diversity and Distributions

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms – Inga Leena Angell – Letters in Applied Microbiology

*Review: The life sulfuric: Microbial ecology of sulfur cycling in marine sediments – Kenneth Wasmund – Environmental Microbiology Reports

Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra – Enrique Zozaya-Valdés – Environmental Microbiology

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds – Christian Wurzbacher – ISME

Built environment

Diversity changes of microbial communities into hospital surface environments – Rika Yano – Journal of Infection and Chemotherapy


A Robust Symmetric Nonnegative Matrix Factorization Framework for Clustering Multiple Heterogeneous Microbiome Data – Yuanyuan Ma – Preprints

Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline – Daniel J. White – Journal of Computational Biology


Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut – Bentley Lim – Cell

‘Genetic scalpel’ can manipulate the microbiome, Yale study shows – Bill Hathaway – Yale News

What is broad-range 16S rDNA PCR? – Amani Patel – Microbiology and Infectious Disease

Microbes in the news

Microbiome: The Body’s Great Conductor –  Conan Milner – Epoch Times

Our Gut Microbes Have Circadian Rhythms, Too — And They Might Own Us – Jesslyn Shields – HowStuffWorks

The Bacteria That Can Help Find Land Mines – Daniel Akst – The Wall Street Journal

Science, publishing, and career

Grant Addresses Computational Challenges in Microbiome Research – Jacobs School of Medicine and Biomedical Science