April 19, 2018

Today we have a few day’s worth of microbiome science to chew on… some interesting skin microbiome studies, bioinformatics publications, and our typical servings of gut /plant-root-soil/animal/water-extremophiles/general microbiome studies.  Dig in!

Events and jobs

Manager, QC Microbiology – Celgene – Phoenix, AZ

Pathology and Microbiology & IPID Graduate Student Research Seminar – UNMC

General microbiome

Cost-benefit analysis of introducing next-generation sequencing (metagenomic) pathogen testing in the setting of pyrexia of unknown origin – Jia Hui Chai – PLOS ONE

* [pre-print] Phylogenetically novel uncultured microbial cells dominate Earth microbiomes – Karen G. Lloyd – bioRxiv

Hologenomics: Systems-Level Host Biology – Kevin R. Theis – mSystems

Antibiotics as Instigators of Microbial Dysbiosis: Implications for Asthma and Allergy – Tomasz P. Wypych – Trends in Immunology

[perspective] Function and functional redundancy in microbial systems – Stilianos Louca – Nature Ecology & Evolution

Human oral microbiome

Comparison of the oral microbiome in mouthwash and whole saliva samples – Xiaozhou Fan – PLOS ONE

Oral Dysbiotic Communities and Their Implications in Systemic Diseases – Preethi Sudhakara – Dentistry Journal

Human skin microbiome

[pre-print] Umbilical Microbiome and Laparoscopic Surgery: A Descriptive Clinical Study – Aiolfi Alberto – Journal of Laparoendoscopic & Advanced Surgical Techniques

The skin microbiome of wound scars and unaffected skin in patients with moderate to severe burns in the subacute phase – Su‐Hsun Liu – Wound Repair and Regeneration

Human gut microbiome

Microbiome-Mediated Bile Acid Modification: Role in Intestinal Drug Absorption and Metabolism – Elaine F. Enright – Pharmacological Research

Non-microbicidal small molecule inhibition of polysaccharide metabolism in human gut microbes: a potential therapeutic avenue – Anthony D. Santilli – ACS Chemical Biology

The Use of Antimicrobials as Adjuvant Therapy for the Treatment of Obesity and Insulin Resistance: Effects and Associated Mechanisms – Sandra Aparecida dos Reis – Diabetes / Metabolism Research and Reviews

Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection – Firas S Midani – The Journal of Infectious Disease

Interactions of Dihydromyricetin, a Flavonoid from Vine Tea (Ampelopsis grossedentata) with Gut Microbiota – Li Fan – Journal of Food Science

Characteristics of the gut microbiota in adult patients with type 1 and 2 diabetes based on the analysis of a fragment of 16S rRNA gene using next-generation sequencing – Dominika Salamon – Polish Archives of Internal Medicine

The Intestinal Microbiota in Colorectal Cancer -Herbert Tilg – Cancer Cell

The Endotoxemia Marker Lipopolysaccharide‐Binding Protein is Reduced in Overweight‐Obese Subjects Consuming Pomegranate Extract by Modulating the Gut Microbiota: A Randomized Clinical Trial – Antonio González‐Sarrías – Molecular Nutrition

Hepatocellular Carcinoma is Associated with Gut Microbiota Profile and Inflammation in Non-Alcoholic Fatty Liver Disease – Francesca Romana Ponziani – Hepatology

Antibiotic‐Associated Disruption of Microbiota Composition and Function in Cirrhosis is Restored by Fecal Transplant – Jasmohan S Bajaj – Hepatology

Does the gastrointestinal microbiome contribute to the “obesity paradox” in melanoma survival? – E A Langan – British Journal of Dermatology

Animal experiments

Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota – Laura J den Hartigh – JN The Journal of Nutrition

Tuna oil alleviate D-galactose induced aging in mice accompanied by modulating gut microbiota and brain protein expression – Dijun Zhang – Journal of Agricultural and Food Chemistry

Dietary Mannan Oligosaccharides Modulate Gut Microbiota, Increase Fecal Bile Acid Excretion, and Decrease Plasma Cholesterol and Atherosclerosis Development – Lisa R. Hoving – Molecular Nutrition

[Review] The Role of the Gut Microbiota in the Metabolism of Polyphenols as Characterized by Gnotobiotic Mice – Pasinetti, Giulio Mari – Journal of Alzheimer’s Disease

Animal microbiome 

Shared larval rearing environment, sex, female size and genetic diversity shape Ae. albopictus bacterial microbiota – Guillaume Minard – PLOS ONE

Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut – Floor Hugenholtz – PLOS ONE

Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE

* Bacterial communities associated with honeybee food stores are correlated with land use – Philip Donkersley – Ecology and Evolution

Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC) – Tara G McDaneld – Journal of Animal Science

Controlling ticks and tick-borne diseases…looking forward – José de la Fuente – Ticks and Tick-borne Diseases

The inside tract: The appendicular, cecal, and colonic microbiome of captive aye‐ayes – Lydia K. Greene – American Journal of Physical Anthropology

Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE

Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production – Lan Mi – Frontiers in Microbiology

Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment – Geon Goo Han – Nature Scientific Reports

Development of the tonsillar microbiome in pigs from newborn through weaning – Luis Carlos Pena Cortes – BMC Microbiology

Plant, root, and soil microbiome

Antimicrobial peptide expression in a wild tobacco plant reveals the limits of host-microbe-manipulations in the field – Arne Weinhold – eLife

Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach – Gui-Hua Lu – Genes

Culture‐independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil‐bioremediation – Narjes Dashti – MicrobiologyOpen

Embracing Community Ecology in Plant Microbiome Research – Francisco Dini-Andreote – Trends in Plant Science

Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil – Felipe Rezende Lima – Brazilian Journal of Microbiology

Soil microbial communities and glyphosate decay in soils with different herbicide application history – Keren Hernández Guijarro – Science of the Total Environment

Shining a light on the dark world of plant root-microbe interactions – Philip Poole – PNAS

Water and extremophile microbiome 

Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico – D. B. Johnson – gebiology

Effect of salinity on diazotrophic activity and microbial composition of phototrophic communities from Bitter-1 soda lake (Kulunda Steppe, Russia) – Zorigto Namsarae – Extremophiles

The ecology and diversity of microbial eukaryotes in geothermal springs – Angela M. Oliverio – The ISME Journal

Built environment

Deposition of Bacteria and Bacterial Spores by Bathroom Hot Air Hand Dryers – Luz del Carmen Huesca-Espitia – American Society for Microbiology

Food microbiology

Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis – Maria Teresa P. Gonçalves – Journal of Food Science

Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR – Andrea Osimani – International Journal of Food Microbiology


Computer-guided design of optimal microbial consortia for immune system modulation – Richard R Stein – eLife

[uncorrected proof] Using pseudoalignment and base quality to accurately quantify microbial community composition – Mark Reppell – PLOS Computational Biology

Fast Metagenomic Binning via Hashing and Bayesian Clustering – Popic Victoria – Journal of Computational Biology

* Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity – Luis M. Rodriguez-R – mSystems

Algorithms and strategies in short‐read shotgun metagenomic reconstruction of plant communities – Robert S. Harbert – Applications in Plant Science

Microbes in the news

Scientists Accidentally Make Plastic-Eating Bacteria Even More Efficient

New York City Mice: Here Are The Bacteria And Viruses That They Carry

Fecal microbiota transplant improves brain function in hepatic encephalopathy

Microbes on the market

Seres Therapeutics (MCRB) Presents New Preclinical Data Supporting the Development of Microbiome Therapeutics for Immuno-Oncology at AACR

Science, publishing, and career

Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses – K. Scott Weber – PLOS ONE

Ed’s non-microbiology picks

News articles below have actual study links inside.

Since 2016, Half of All Coral in the Great Barrier Reef Has Died

Marijuana’s effects on young brains diminish 72 hours after use, research says

Cannabinoids are easier on the brain than booze, study finds

Stem cell treatment drastically reduces drinking in alcoholic rats

The Ecology Of Disadvantage: Obesity Is Not Randomly Distributed Across The U.S., According To New Study

How your next meal could help fight depression, stress

Study: People with less political knowledge think they know a lot about politics


April 17, 2018

Today’s Digest is brief, but not without highlights. Brazilian and MIT scientists created artificial antimicrobial peptides using computer algorithms, ecologists model intransitive competition, and we urgently need to tackle flesh-eating bacteria. In addition, do check out several new issues’ table of contents now, if you have access.

General microbiology

** In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design – William F. Porto et al. – Nature Communications

Press: Artificial antimicrobial peptides could help overcome drug-resistant bacteria – Anne Trafton – MIT News

Memories Are Made of This: Bacteria Remember Who Their Enemies Are with CRISPRs – Marcia Stone – BioScience

Human gut microbiome

Review: Drug‐induced enterocolitis: Prevention and management in primary care – Ignazio Grattagliano et al. – Journal of Digestive Diseases

Journal of Gastroenterology and Hepatology – Issue Information – TOC

Animal experiments

Gnotobiotic and Conventional Mouse Systems to Support Microbiota Based Studies – Richard Lavin et al. – Current Protocols in Immunology

Food Microbiology

Journal of Food Science – Issue Information – TOC

Plant, root and soil microbiome

Commentary: Taking the step: from Evo‐Devo to plant–microbe interaction evolution with the liverwort Marchantia – Mélanie Rich and Pierre‐Marc Delaux – New Phytologist

** Intransitive competition is common across five major taxonomic groups and is driven by productivity, competitive rank and functional traits – Santiago Soliveres et al. – Journal of Ecology

Preprint: Phylogenomics reveals dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism – Steven A Higgins et al. – bioRxiv

Phages and viruses

Preprint: Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut – Emma Guerin et al. – bioRxiv

Preprint: Modelling phage-bacteria interactions driving predation and horizontal gene transfer – Jorge Moura de Sousa et al. – bioRxiv

Microbes in the news

Could Microbiota Predict Response to Anti-TNF Agents in Spondyloarthritis? – Kelly Davio – The Center for Biosimilars

You cannot escape poop bacteria – Sara Chodosh – Popular Science

Scientists Want to Replace Pesticides With Bacteria – Elizabeth G Dunn – Bloomberg Businessweek

Spikes of graphene can kill bacteria on implants – Science Daily

** Flesh-eating bacteria cases on the rise and we need an urgent response – Daniel O’Brien – The Conversation

Bacteria and feces found in fake cosmetics similar to popular makeup brands – Miriam Hernandez – ABC13

BESSY II sheds light on how the internal compass is constructed in magnetotactic bacteria – Science Daily

Connection Between Gut Bacteria And Autoimmunity Strengthens – Julianna LeMieux – American Council on Science and Health

In pictures: The bacteria living on your hands right now – Gaya Chandramohan – Channel NewsAsia

16 April, 2018

Today’s digest is packed with exciting research on links between gut microbiome and bone generation/development, also an interesting approach to fecal metabolome sampling

Gut Microbiome

Gut Microbiome and Bone.Ibáñez L. Joint Bone Spine

The protective effect of Lactobacillus and Bifidobacterium as the gut microbiota members against chronic urticaria.Rezazadeh A. International Immonopharmacology

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.Pan WH. Genome Medicine

Fecal Microbiome

Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection.Seekatz AM. Anaerobe

Clostridium difficile stool shedding in infants hospitalized in two neonatal intensive care units is lower than previous point prevalence estimates using molecular diagnostic methods.Hines AG. BMC Pediatrics


Plant, Soil, and Water Microbiome

Metataxonomy and functionality of wood-tar degrading microbial consortia.Brusetti L. Journal of Hazardous Materials

In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments.Xie Y. Environmental Pollution

Biogas production and microbial community properties during anaerobic digestion of corn stover at different temperatures.Liu C. Bioresource Technology

Cadmium exposure and <i>Sedum alfredii</i> planting interactions shape the bacterial community in rhizosphere of the hyperaccumulator plant. Hou D. Applied Environmental Microbiology

Animal Experiments and Microbiome

The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria. Jung DH. Applied Microbiology and Biotechnology

Comparative biogeography of the gut microbiome between Jinhua and Landrace pigs.Xiao Y. Scientific Reports

Changes in the Rumen Epithelial Microbiota and Host Gene Expression of Cattle in Response to Alterations in Dietary Carbohydrate Composition.Petri RM. Applied Environmental Microbiology


Mercury methylating microbial communities of boreal forest soils

Jingying Xu. bioRxiv


Rat Fecal Metabolomics-Based Analysis.Deda O. Methods in Molecular Biology: Metabolic Profiling


Correction: <i>’Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance</i>.British Journal of Sports Medicine

15 April, 2018

Today’s digest features an interesting article on microbial resevoirs in an urban setting, and influence of sequencing depth in chareterising the resistome .

General Microbiome

Diversity of the midstream urine microbiome in adults with chronic kidney disease.Kramer H. International Urology and Nephrology

Oral/Gut Microbiome

Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome.Laudadio I. OMICS

The role of the gut microbiota in the pathology and prevention of liver disease.Altamirano-Barrera A. Journal of Nutritional Biochemistry

Effects of green tea on miRNA and microbiome of oral epithelium.Adami GR. Scientific Reports

Plant, Soils, and Water Microbiome

High-throughput sequencing reveals microbial communities in drinking water treatment sludge from six geographically distributed plants, including potentially toxic cyanobacteria and pathogens.Xu H. Science of Total Environment

Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity.Charlop-Powers Z. PNAS

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.Mandakovic D. Scientific Reports

Multivariate relationships between microbial communities and environmental variables during co-composting of sewage sludge and agricultural waste in the presence of PVP-AgNPs.Zhang L. Bioresources Technology

Animal Experiments and Microbiome

Gut microbiota recovery and immune response in ampicillin-treated mice.Castro-Mejía JL. Research in Veterinary Sciences

When the Nose Doesn’t Know: Canine Olfactory Function Associated With Health, Management, and Potential Links to Microbiota.Jenkins EK. Frontiers in Veterinary Sciences


Microbiota transplantation and/or CRISPR-Cas in the battle against antimicrobial resistance.Vila J. Clinical Microbiology and Infection

Impact of sequencing depth on the characterization of the microbiome and resistome.Zaheer R. Scientific Reports

April 13, 2018

Today’s digest is short and sweet, but includes exciting science that explores how a vegan diet modulates the gut microbiome and new techniques for detection of DNA SNIPs.

General Microbiome

Effect of nisin on microbiome-brain-gut axis neurochemicals by Escherichia coli-induced diarrhea in mice.Jia Z. Microbial Pathogenesis

Food for Gut: Microbiota Fuels Immune Reconstitution after BMT.Simms-Waldrip TR. Cell Host and Microbe


Oral/Gut Microbiome

Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids.Martinez-Guryn K. Cell Host and Microbe

Impact of a vegan diet on the human salivary microbiota. Hansen TH. Scientific Reports


Plant, Soils, and Water Microbiome

Bacterial communities of four adjacent fresh lakes at different trophic status. Ji B. Ecotoxicology and Environmental Safety

Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes.Wille L. Plant, Cell and Environment

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome.Daleo P. Ecology

Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance.Ye F. Microbial Ecology

d-Amino Acids Are Exuded by Arabidopsis thaliana Roots to the Rhizosphere.Hener C, Hummel S. International Journal of Molecular Sciences


Animal Microbiome and Experiments

Characterization of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins.Salami SA. FEMS Microbiology Ecology

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.Thies S. Scientific Reports

Pasture Feeding Changes the Bovine Rumen and Milk Metabolome.O’Callaghan TF. Metabolites

Microbial metabolites, short-chain fatty acids, restrain tissue bacterial load, chronic inflammation, and associated cancer in the colon of mice.Kim M. European Journal of Immunology

Molecular diversity of the faecal microbiota of Toy Poodles in Japan.Omatsu T. Journal of Veterinary Medicine


SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.Youngblut ND. Frontiers in Microbiology

April 12, 2018

Of note today: non-exclusive breastfeeding increases the risk of HIV transmission via the alteration of gut microbiome/T-cell activation; Fasting altered the gut microbiome in beneficial ways but only in mice previously fed a high fat diet; An investigation into new species of the honey and bumblebee gut commensal genus Gilliamella; Catfish development shapes gut microbial community structure independent of diet; A metagenomic analysis of the skin microbiome of the frog, Craugastor fitzingeri; The microbiome is altered during the bioremediation of herbicide contaminated soil; The impact of urban density on the soil microbiome; A randomized placebo controlled clinical trial of a microbiota based drug for the prevention of Clostridium difficile Infection; and the virome of the Cuatro Ciénegas Basin of Mexico

Pregnancy and early life

*Feeding-related gut microbial composition associates with peripheral T cell activation and mucosal gene expression in African infants – Lianna F Wood – Clinical Infectious Diseases

Comparative Analysis of Gut Microbial Communities in Children under 5 Years Old with Diarrhea – Hongyu Wen – Journal of Microbiology and Biotechnology

Review: Microbiome in Embryonic Implantation and Implantation Failure – Jason M. Franasiak – Recurrent Transplant Failure

Human oral microbiome

The cultivable bacterial flora of the esophagus in subjects with esophagitis – Elisabeth Norder Grusell – Scandinavian Journal of Gastroenterology

Human urogenital microbiome

The upper and lower tract urinary microbiomes of stone formers are similar: a pilot study – Heiko Yang – The Journal of Urology

Human gut microbiome

Shifts in the gut microbiota structure caused by Helicobacter pylori eradication therapy – Evgenii I – bioRxiv

The microbial metabolite TMAO in association with inflammation and microbial dysregulation in three HIV cohorts at various disease stages – Catharina Missailidis – AIDS

Review: Microbiome-Mediated Upregulation of MicroRNA-146a in Sporadic Alzheimer’s Disease – Yuhai Zhao – Frontiers in Neurology

Review: Interplay Between the Gut-Brain Axis, Obesity and Cognitive Function – Ana Agustí – Frontiers in Neuroscience

Review: The Brain–Intestinal Mucosa–Appendix– Microbiome–Brain Loop – Luis Vitetta – Diseases

Review: New Therapeutic Drugs from Bioactive Natural Molecules: the Role of Gut Microbiota Metabolism in Neurodegenerative Diseases – Francesco Di Meo – Current Drug Metabolism

Review: Microbial Effects on Immunity in HIV: Virus, Gender or Sexual Preference Induced? – Nichole R. Klatt – EBioMedicine

Review: Microbiome and Gut Dysbiosis – José E. Belizário – Metabolic Interaction in Infection

Review: Clostridium Bacteria and Autism Spectrum Conditions: A Systematic Review and Hypothetical Contribution of Environmental Glyphosate Levels – Isadora Argou-Cardozo  – Medical Science

Review: Current State of Knowledge on Implications of Gut Microbiome for Surgical Conditions – Edmund B. Chen – Journal of Gastrointestinal Surgery

Review: Maintenance of intestinal homeostasis by mucosal barriers – Ryu Okumura – Inflammation and Regeneration


Animal experiments

*Food withdrawal alters the gut microbiota and metabolome in mice – Xiaojiao Zheng – The FASEB Journal

Animal microbiome

*Addressing the diversity of the honeybee gut symbiont Gilliamella: description of Gilliamella apis sp. nov., isolated from the gut of honeybees (Apis mellifera) – Jane Ludvigsen – International Journal of Systematic and Evolutionary Microbiology

*Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water – Zhimin Zhang – Frontiers in Microbiology

*The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data – Eria A. Rebollar – Frontiers in Microbiology

Gut Microbiota-Regulated Pharmacokinetics of Berberine and Active Metabolites in Beagle Dogs After Oral Administration – Ru Feng – Frontiers in Pharmacology

Strongyle Infection and Gut Microbiota: Profiling of Resistant and Susceptible Horses Over a Grazing Season – Allison Clark – Frontiers in Physiology

Review: Opinion: Pesticides Could Alter Amphibian Skin Microbiomes and the Effects of Batrachochytrium dendrobatidis – Krista A. Mccoy – Frontiers in Microbiology

Preprint: Earthworms and Cadmium – heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils? – Maja Šrut – bioRxiv

Effect of Dietary Non-phytate Phosphorus Levels on the Diversity and Structure of Cecal Microbiota in Meat Duck from 1 to 21 d of age – S J Dai – Poultry Science

Rumen bacterial community structure impacts feed efficiency in beef cattle – Henry A Paz – Journal of Animal Science

Responses in the rumen microbiome of Bos taurus and indicus steers fed a low-quality rice straw diet and supplemented protein  – E A Latham – Journal of Animal Science

Plant, root, and soil microbiome

*Dynamic changes in microbial communities during the bioremediation of herbicide (chlorimuron-ethyl and atrazine) contaminated soils by combined degrading bacteria – Jian Wang – PLOSone

Comparison of Microbial Community Structure in Kiwifruit Pollens – Min-Jung Kim – The Plant Pathology Journal

*Soil Bacterial Diversity Is Associated with Human Population Density in Urban Greenspaces – Haitao Wang – Environmental Science and Technology

Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China – Baihui Ren – Scientific Reports

Preprint: Social Motility: Interaction between two sessile soil bacteria leads to emergence of surface motility – Lucy M McCully – bioRxiv

Water and extremophile microbiome

Sulphate-reducing bacteria (SRB) in the Yangtze Estuary sediments: Abundance, distribution and implications for the bioavailibility of metals – Zuo-shun Niu – Science of The Total Environment

Bacterial community succession and degradation patterns of hydrocarbons in seawater at low temperature – Leendert Vergeynst – Journal of Hazardous Materials

Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition – Emily B. Graham – PeerJ

Organic carbon source and salinity shape sediment bacterial composition in two China marginal seas and their major tributaries – Kai Wang – Science of The Total Environment

Nitrate amendment reduces biofilm biomass and shifts microbial communities in remote, oligotrophic ponds – Carmella Vizza – Freshwater Science

Microbial Ecology

Bacterial interspecies quorum sensing in the mammalian gut microbiota – Karina Bivar Xavier – Comptes Rendus Biologies

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass – Aoife Joyce – Frontiers in Microbiology


Probiotics / prebiotics

*Results from a Randomized Placebo-Controlled Clinical Trial of a RBX2660—a Microbiota-based Drug for the Prevention of Recurrent Clostridium difficile Infection – Erik R Dubberke – Clinical Infectious Dieases

Outer Membrane Vesicles From Probiotic and Commensal Escherichia coli Activate NOD1-Mediated Immune Responses in Intestinal Epithelial Cells – María-Alexandra Cañas – Frontiers in Microbiology

Fecal Transplants

Recruitment of feces donors among blood donors: Results from an observational cohort study – Simon Mark Dahl Jørgensen – Gut Microbes

Fecal microbiota transplantation associated with 10 years of stability in a patient with SPMS – Seraj Makkawi – Neurology, Neuroimmunology & Neuroinflammation

Phages and viruses

Metagenomic analysis of ssDNA viruses in surface seawater of Yangshan Deep-Water Harbor, Shanghai, China – Hongming Wang – Marine Genomics

*The viral structure of the Cuatro Ciénegas Basin, a unique oasis in Northern Mexico, reveals a highly diverse population at a small geographic scale – B. Taboada – Applied and Environmental Microbiology

Waste and Pollution

Metataxonomy and functionality of wood-tar degrading microbial consortia – Lorenzo Brusetti – Journal of Hazardous Materials

Variations in the denitrifying microbial community and functional genes during mesophilic and thermophilic anaerobic digestion of cattle manure – Kaiyu Zhang – Science of The Total Environment


Electrochemical detection of viable bacteria in urine and antibiotic selection – Noriyuki Nakamura – Biosensors and Bioelectronics


Microbes in the news

Nova-like explosion of spinning live bacteria explained – A’ndrea Elyse Messer – Phys.org

New ‘NanoZymes’ use light to kill bacteria – Science Daily

The Germs That Love Diet Soda – Moises Velasquez-Manoff

Bacteria can pass on memory to descendants, researchers discover – Melody Pupols – Phys.org

Charting an underexplored landscape: The genitourinary microbiome – Medical Press

April 10, 2018

After a brief hiatus, your Digest is back! After screening several hundred papers, progress seems to concentrate on a selected fields, including human gut microbiome and plant/soil microbiome. The WHO advocates for a global atlas of zoonotic viruses, a PDF link to a book volume full of application of microbiome engineering in agriculture, environmental protection and industry, and 16s rDNA primers can cross-react with mitochondrial sequences in eukaryotic cells. Last but not least, what can we all do to help young scientists, including ourselves, cope with immense pressure and distress?

General microbiology

Role of Partially Saturated Canthaxanthin and Ergosterol in the Survival of Aspergillus carbonarius Mutant at Extreme Acidic Condition – A. Kumar et al. – Microbiology

Coupled iron-microbial catalysis for CO2 hydrogenation with multispecies microbial communities – Elise Blanchet et al. – Chemical Engineering Journal

An integrated membrane bioreactor system with iron-dosing and side-stream co-fermentation for enhanced nutrient removal and recovery: System performance and microbial community analysis – Ruo-hong Li et al. – Bioresource Technology

The Microbiome and Population Health: Considerations to Enhance Study Design and Data Analysis in Observational and Interventional Epidemiology – Ryan T Demmer – American Journal of Epidemiology

Robust, linear correlations between growth rates and β-lactam–mediated lysis rates – Anna J. Lee et al. – PNAS USA

Human oral microbiome

Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing – Federico Mussano and Ilario Ferrocino et al. – BMC Oral Health

Human gut microbiome

A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt and Hazel Poyntz et al. – Clinical & Translational Immunology

Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction – Xin Zhou, Jing Li and Junli Guo et al. – Microbiome

Book chapter: Influence of the Gut Microbiome on Immune Development During Early Life – Shankar S. Iyer and Richard S. Blumberg – Physiology of the Gastrointestinal Tract (Sixth Edition)

Book chapter: Gut Barrier: Innate Immunity – Gerco den Hartog et al. – Physiology of the Gastrointestinal Tract (Sixth Edition)

Review: Molecular Pathophysiology of Epithelial Barrier Dysfunction in Inflammatory Bowel Diseases – Jessica Y. Lee et al. – Proteomes

Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo – Alba C. Mayta-Apaza et al. – The Journal of Nutritional Biochemistry

Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls – Qi-Xiang Mei et al. – Pancreatology

Human multi-site microbiome

Microbiota potential for the treatment of sexual dysfunction – Hassan Tirandaz et al. – Medical Hypotheses

Animal experiments

Nile tilapia: Effects of Lactogen 13, a New Probiotic Preparation, on Gut Microbiota and Endocrine Signals Controlling Growth and Appetite of Oreochromis niloticus Juveniles – Gioacchini Giorgia et al. – Microbial Ecology

Effects of shenling baizhu powder herbal formula on intestinal microbiota in high-fat diet-induced NAFLD rats – Yupei Zhang et al. – Biomedicine & Pharmacotherapy

Gut Microbiota Promotes Tumor Growth in Mice by Modulating Immune Response – Vrishketan Sethi et al. – Gastroenterology

The effects of feeding monensin on rumen microbial communities and methanogenesis in bred heifers fed in a drylot – E.A. Melchior et al. – Livestock Science

Identification, characterization and selection of autochthonous lactic acid bacteria as probiotic for feedlot cattle – Natalia C. Maldonado et al. – Livestock Science

Glyphosate based- herbicide exposure affects gut microbiota, anxiety and depression-like behaviors in mice – Yassine Aitbali et al. – Neurotoxicology and Teratology

Animal microbiome

Characterization of the bacterial community in different parts of the gut of sea cucumber (Apostichopus Japonicus) and its variation during gut regeneration – Luo Wang et al. – Aquaculture Research

Review: The adherence and colonization of microorganisms in fish gastrointestinal tract – Xuemei Li et al. – Reviews in Aquaculture

Effect of Saccharomyces boulardii and Bacillus subtilis B10 on gut microbiota modulation in broiler – Chubin Qin and Li Gong et al. – Animal Nutrition

Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp. – Thao V. Nguyen et al. – Marine Biotechnology

Review: Use of antibiotics in broiler production: Global impacts and alternatives – Youcef Mehdi et al. – Animal Nutrition

Food Microbiome

PDF: High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Bean Fermentation – Dão Pedro de Carvalho Neto et al. – Food Technology and Biotechnology

The impact of vegan production on the kimchi microbiome – Michelle Zabat et al. – Food Microbiology

Plant, root and soil microbiome

Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure – Sonya Erlandson et al. – Molecular Ecology

RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi – Ko‐Hsuan Chen et al. – New Phytologist

Microbial diversity changes with rhizosphere and hydrocarbons in contrasting soils – Muhammad Atikul Islam Khan et al. – Ecotoxicology and Environmental Safety

Effects of redox potential on soil Cadmium solubility: Insight into microbial community – Delong Meng et al. – Journal of Environmental Sciences

Long-term phosphorus application to a maize monoculture influences the soil microbial community and its feedback effects on maize seedling biomass – Ming Lang et al. – Applied Soil Ecology

Book chapter: Differential Responses of Plants to Biotic Stress and the Role of Metabolites – Maham Saddique et al. – Plant Metabolites and Regulation Under Environmental Stress

Role of Phenolic Acids from the Rhizosphere Soils of Panax notoginseng as a Double-Edge Sword in the Occurrence of Root-Rot Disease – Ya-Meng Zhao et al. – Molecules

Forum: From Petri Dishes to Model Ecosystems – Oskar Siemianowski et al. – Trends in Plant Science

An Insight into Catechins Metabolic Pathways of Camellia sinensis Based on Genome and Transcriptome Analysis – Wenzhao Wang et al. – Journal of Agricultural and Food Chemistry

Seasonal characterization of sugarcane vinasse: Assessing environmental impacts from fertirrigation and the bioenergy recovery potential through biodigestion – Lucas Tadeu Fuess et al. – Science of The Total Environment

Soil microbial biomass: A key soil driver in management of ecosystem functioning – Jay Shankar Singh and Vijay Kumar Gupta – Science of The Total Environment

Phosphorus fertilising potential of fly ash and effects on soil microbiota and crop – Deborah Schönegger et al. – Resources, Conservation and Recycling

Response of the soil microbial community to different fertilizer inputs in a wheat-maize rotation on a calcareous soil – Shuikuan Bei et al. – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

Bacterial Diversity and Functional Activity of Microbial Communities in Hot Springs of the Baikal Rift Zone – E. V. Lavrentyeva et al. – Microbiology

Microbial Community Composition and Rates of the Methane Cycle Microbial Processes in the Upper Sediments of the Yamal Sector of the Southwestern Kara Sea – A. S. Savvichev et al. – Microbiology

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats – Taruna Schuelke et al. – Molecular Ecology

Discriminating activated sludge flocs from biofilm microbial communities in a novel pilot-scale reciprocation MBR using high-throughput 16S rRNA gene sequencing – Ryan De Sotto et al. – Journal of Environmental Management

PDF: Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system – Duntao Shu et al. – Bioresource Technology

Antibiotic resistance in wastewater treatment plants: Tackling the black box – Célia M. Manaia et al. – Environment International

Phages and viruses

** Building a global atlas of zoonotic viruses – Dennis Carroll et al. – Bulletin of WHO

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes – Jeffrey K. Cornuault et al. – Microbiome

Dual Insect specific virus infection limits Arbovirus replication in Aedes mosquito cells – Michaela J. Schultz et al. – Virology


** Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run – Yi-Chun Yeh et al. – mSystems

Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method – Xinxu Zhang et al. – Applied and Environmental Microbiology

Clinical impact of rapid bacterial identification by MALDI-TOF MS combined with the bêta-LACTA™ test on early antibiotic adaptation by an antimicrobial stewardship team in bloodstream infections – A. Mizrahi et al. – Infectious Diseases

Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids – Sean P. Leonard et al. – ACS Synthetic Biology

** Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers to Eukaryotic DNA: Mistaken Microbial Community Profiling in Environmental Samples – Shailendra Yadav et al. – Current Microbiology

Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods – Dongxue Zhang et al. – Analytical Chemistry

** Book chapter PDF: Microbial, Plant, Environmental and Industrial Technologies – Debmalya Barh and Vasco Azevedo – Microbial Omics: Applications in Biotechnology

Metabolome- and genome-scale model analyses for engineering of Aureobasidium pullulans to enhance polymalic acid and malic acid production from sugarcane molasses – Jun Feng and Jing Yang et al. – Biotechnology for Biofuels

eDNA-based bioassessment of coastal sediments impacted by an oil spill – Yuwei Xie et al. – Environmental Pollution

Using natural biomass microorganisms for drinking water denitrification – Darleila Damasceno Costa et al. – Journal of Environmental Management


Cluster and Multiple Correspondence Analyses in Rheumatology: Paths to Uncovering Relationships in a Sea of Data – Lu Han et al. – Rheumatic Disease Clinics of North America

Microbes in the news

Faecal transplantation: do not try this at home – Talha Khan Burki – The Lancet Gastroenterology & Hepatology

Non-microbiology picks

** Editorial: Time to talk about why so many postgrads have poor mental health – Nature

Editorial: Using Preprints for Journal Clubs – Arturo Casadevall and Neil Gow – mBio