The Microbiome Digest Team

Hi all, it’s Elisabeth Bik, doing a rare blog post here, after having run this blog for 3 years in a row. I am having a blast working at uBiome, but as I wrote in January, with my long commute and continuing science integrity work I can not spend much time here at Bik’s Picks. Fortunately, the Microbiome Digest has been able to continue to run through the fantastic work of a group of 20 people from all over the world. In the last couple of months, some new people joined, and some other people left, so it was time for a update on the team members and their background and interest. I am so grateful that this team could take over from me, and that they are running the blog so I can currently focus on other things.

So here is the new Microbiome Digest Team page where you can read more about the fantastic group of scientists who are currently writing the Microbiome Digest posts.

Thank you all, team, for providing this continuous stream of new microbiome papers and articles.




September 13,2017

Our midweek digest is a treat for wine drinkers- two studies looking at vineyard microbiomes and news of how Nestlé is moving into microbiome research. Lastly, read about an exciting workflow that makes it easier to map the resistome.

General Microbiome

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles.

Parnell LA .Scientific Reports

Human gut microbiome

Host-microbe interaction in the gastrointestinal tract.

Parker A.Environmental Microbiology Report

Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients.

Ticinesi A.Scientific Reports

Microbes in Infant Gut Development: Placing Abundance Within Environmental, Clinical and Growth Parameters.

Obermajer T.Scientific Reports

Animal experiments and microbiome

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models.

Cekanaviciute E, PNAS

The microbiota influences cell death and microglial colonization in the perinatal mouse brain.

Castillo-Ruiz A. Brain, Behaviour, and Immunity

Microbial colonization is required for normal neurobehavioral development in zebrafish.

Phelps D,.Scientific Reports


Ozone-cathode microbial desalination cell; An innovative option to bioelectricity generation and water desalination.

Gholizadeh A. Chemosphere.

Plant and soil microbiome

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.

Mezzasalma V. PLoS One.

Is microbial terroir related to geographic distance between vineyards?

Miura T. Environmental Microbiology Reports

Bacteria utilising plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil.

Uksa M. Environmental Microbiology Reports

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions.

Bailly A. Frontiers in Microbiology

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis.

Michas A. Microbiome

Lung Microbiome

Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence.

Miranda-CasoLuengo AA.BMC Genomics

Mechanistic insight into the function of the microbiome in lung diseases.

Ubags NDJ. European Respiratory Journal


A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity.

Ruiz VE.Nature Communications


The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening.

Earls MR. PLoS One

Rapid resistome mapping using nanopore sequencing.

van der Helm E.Nucleic Acids Research  

Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms

Wang J. PNAS


Nestlé moves into gut microbiome tests.

News- Nature Biotechnology


Shotgun metagenomics, from sampling to analysis.

Quince C,Nature Biotechnology


Erratum to: Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Hale VL. Microbial Ecology

September 12, 2017

Today’s post is short and sweet. A European Food Safety Authority panel releases a report on deoxynivalenol (DON), a review on the effects of obesity on depression, and fish oil might be good for your gut microbiota.

General microbiology

Viable But Non-Culturable Cells Are Persister Cells – Jun-Seob Kim et al. – bioRxiv

Regulated release of cryptococcal polysaccharide drives virulence and suppresses immune cell infiltration into the central nervous system – Steven T. Denham et al. – bioRxiv

*Scientific Opinion: Risks to human and animal health related to the presence of deoxynivalenol and its acetylated and modified forms in food and feed – EFSA Panel on Contaminants in the Food Chain et al. – EFSA Journal

Strategies for editing virulent staphylococcal phages using CRISPR-Cas10 – S.M. Nayeemul Bari et al. – ACS Synthetic Biology

Compensatory evolution facilitates the acquisition of multiple plasmids in bacteria – Alfonso Santos-Lopez et al. – bioRxiv

Human gut microbiome

The Role of Gut Microbiome in the Pathogenesis of Prostate Cancer: a Prospective, Pilot Study – Golombos DM et al. – Urology

Review: Pathogenesis of Helicobacter pylori infection – Vania Camilo et al. – Helicobacter

Helicobacter Special Issue: XXXth International Workshop on Helicobacter & Microbiota in Inflammation & Cancer

*Biological and clinical implications of herbal medicine and natural products for the treatment of inflammatory bowel disease – Bao-Jian Guo et al. – Annals of The New York Academy of Sciences

Plant non-starch polysaccharides that inhibit key enzymes linked to type 2 diabetes mellitus – Dan Liu et al. – Annals of The New York Academy of Sciences

Mini-Review: Role of microbiota in the pathogenesis of functional disorders of the lower GI tract: Work in progress – Jonna Jalanka and Robin Spiller – Neurogastroenterology and Motility

*Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women – Cristina Menni et al. – Scientific Reports

Press: Omega 3 helps the gut stay healthy, study finds – Medical Xpress

Human gut-microbiome-brain axis

*Review: Effects of obesity on depression: a role for inflammation and the gut microbiota – Schachter J et al. – Brain, Behavior, and Immunity

Preimmunization with a heat-killed preparation of Mycobacterium vaccae enhances fear extinction in the fear-potentiated startle paradigm – Fox JH et al. – Brain, Behavior, and Immunity

Animal experiments

Rapamycin treatment attenuates age-associated periodontitis in mice – An JY et al. – Geroscience

Animal microbiome

Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease – Zeineldin M et al. – Veterinary Microbiology

Increased microbiome diversity at the time of infection is associated with improved growth rates of pigs after co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) – Ober RA et al. – Veterinary Microbiology

Plant, root and soil microbiome

Seasonal and inter-annual variability in litter decomposition and nitrogen availability in a mid-Appalachian watershed – Jeff W. Atkins et al. – Ecosphere

Probiotics, Prebiotics and Synbiotics

Probiotic Supplementation in Chronic Kidney Disease: A Double-blind, Randomized, Placebo-controlled Trial – Borges NA et al. – Journal of Renal Nutrition

Apple pectin-derived oligosaccharides produce carbon dioxide radical anion in Fenton reaction and prevent growth of Escherichia coli and Staphylococcus aureus – Martinov J et al. – Food research international

Microbes in the news

Researchers found omega 3 helps the gut stay healthy – Pharmabiz

Microbes on the market

Tata and OptiBiotix seal deal for India prebiotic expansion – Gary Scattergood+ – Food Navigator Asia

Startups focus on the microbiome – Olivia Tucker – Version Weekly


September 4, 2017

Interaction of gut microbiota metabolites with host chromatin, modulation of T cell responses by Propionibacterium acnes in healthy and diseased skin, metatranscriptomics of the termite gut microbiota.

Multi-site human microbiome

Review: The potential of the microbiota to influence vaccine responses – David J Lynn – Journal of Leukocyte Biology

Human skin microbiome

Phenotype and antimicrobial activity of Th17 cells induced by Propionibacterium acnes strains associated with healthy and acne skin – George W Agak – Journal of Investigative Dermatology

Human gut microbiome

Review: The intricate connection between diet, microbiota, and cancer: A jigsaw puzzle – Melek Canan Arkan – Seminars in Immunology

Animal experiments

Characterization of vaginal microbiota of endometritis and healthy sows using high-throughput pyrosequencing of 16S rRNA gene – Jun Wang – Microbial Pathogenesis

Paneth Cell Defects Induce Microbiota Dysbiosis In Mice And Promote Visceral Hypersensitivity – Ambre Riba – Gastroenterology

Novel Interactions between Gut Microbiome and Host Drug-processing Genes Modify the Hepatic Metabolism of the Environmental Chemicals PBDEs – Cindy Yanfei Li – Drug Metabolism and Disposition

Fecal microbiota of lambs fed purple prairie clover (Dalea purpurea Vent.) and alfalfa (Medicago sativa) – Qianqian Huang – Archives of Microbiology

Effect of dietary copper level on the gut microbiota and its correlation with serum inflammatory cytokines in Sprague-Dawley rats – Feng Zhang – Journal of Microbiology

Animal microbiome

Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome – Martyna Marynowska – BMC Genomics

Plant, root, and soil microbiome

Review: Wetland management using microbial indicators – Hidetoshi Urakawa – Ecological Engineering

Impacts of Repeated Glyphosate Use on Wheat-Associated Bacteria are Small and Depend on Glyphosate-Use History – Daniel C Schlatter – Applied and Environmental Microbiology

Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest – Can Du – Journal of Microbiology

Water and extremophile microbiome

Antibiotic resistance genes in an urban river as impacted by bacterial community and physicochemical parameters – Zhen-Chao Zhou – Environmental Science and Pollution Research


Intestinal Microbiota in Infants at High-risk for Allergy: Effects of Prebiotics and Role in Eczema Development – Harm Wopereis – Journal of Allergy and Clinical Immunology


Review: Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin – Kimberly A Krautkramer – Translational Research

Microbes in the news

Baby bottle dish soap recalled due to harmful bacteria in the soap – ABC Action News

Microbes on the market

This Biotech Clothing Automatically Ventilates When You Start to Sweat – Kyree Leary – Futurism

September 2, 2017

General microbiome

Nutrient stoichiometry shapes microbial coevolution – ML Larsen – bioRxiv

Review: Interplay of innate lymphoid cells and the microbiota – L Britanova – Immunological Reviews



Human gut microbiome

The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens – S Kim – Immunological Reviews


Animal experiments

Effect of Propionibacterium acidipropionici P169 on the rumen and faecal microbiota of beef cattle fed a maize-based finishing diet – E Azad – Beneficial Microbes

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – L Chi – Toxicological Sciences


Animal microbiome 

Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients – MC Hughey – PeerJ

Effects of probiotic on microfloral structure of live feed used in larval breeding of turbot Scophthalmus maximus – Y Jiang – Chinese Journal of Oceanology and Limnology


Plant, root, and soil microbiome

Synergistic rhizosphere degradation of γ-hexachlorocyclohexane (lindane) through the combinatorial plant-fungal action – MD Asemoloye – PLoS One

Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil – AK Borsodi – International Journal of Systematic and Evolutionary Microbiology


Water microbiome and extremophiles 

Natronoarchaeum persicum sp. nov., a haloarchaeon isolated from a hypersaline lake – A Naghoni – International Journal of Systematic and Evolutionary Microbiology

Geographical variations in bacterial communities associated with soft coral Scleronephthya gracillimum – S Woo – PLoS One

Biogeochemical conversion of sulfur species in saline lakes of Steppe Altai – SV Borzenko – Chinese Journal of Oceanology and Limnology

Role of heavy metals in structuring the microbial community associated with particulate matter in a tropical estuary – VA Sheeba – Environmental Pollution


Probiotics / prebiotics

Review: To add or not to add probiotics to infant formulae? An updated systematic review – A Skórka – Beneficial Microbes


Phages and viruses

Biogeography & Environmental Conditions Shape Phage & Bacteria Interaction Networks Across The Human Microbiome – GD Hannigan – bioRxiv

ReviewImpact of transmission cycles and vector competence on global expansion and emergence of arboviruses – A Agarwal – Reviews in Medical Virology



Validation of RT-qPCR approaches to monitor Pseudomonas syringae gene expression during infection and exposure to pattern-triggered immunity – A Smith – bioRxiv

Review: Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes – T Clavel – Immunological Reviews


Microbes in the news 

Could an altered microbiome predict Parkinson’s disease – Nutra Ingredients

Could faecal microbiota transplantation be used to tackle asthma – Nutra Ingredients

Probiotics effective in preventing sepsis in infants – Healio

Start made on revealing scale of gut bugs’ hijacking our signalling – Chemistry World

Dietary Indoles May Help Extend Lifespan – Emax Health

Baby Bottle Soap Recalled Due to ‘Harmful Bacteria’ – Fortune

Multi-drug resistant bacteria proliferating through poultry waste – TOI


September 1, 2017

A rich Digest to start your September. A special issue of Immunological Reviews on the host-microbiome interaction, water can be dangerous – both in Texas and your washing machines, and how about some music inspired by the microbiome?


Microbiology jobs in Kansas – New Scientist Jobs

Post Doctoral Researcher – The Ohio State University

Laboratory Assistant III – Microbiology – Contingent – Allegiance Health – Jackson, MI

Microbiology Lab Technician (Up to $2500, Global MNC, No experience required)

General microbiology

Towards a universal molecular microbiological test – Richard J. N. Allcock et al. – Journal of Clinical Microbiology

Human microbiome inspired antibiotics with improved β-lactam synergy against MDR Staphylococcus aureus -Chu J et al. – ACS Infectious Diseases

Pregnancy and early life

Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months – Floor Hugenholtz et al. – International Journal of Microbiology

Human skin microbiome

Application of sebomics for the analysis of residual skin surface components to detect potential biomarkers of type-1 diabetes mellitus – Satyajit S. Shetage et al. – Scientific Reports

Human near-sterile sites

Bone Remodeling and the Microbiome – Pacifici R – Cold Spring Harbor Perspectives in Medicine

Human lung microbiome

Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients – Solveig Tangedal et al. – Respiratory Research

Human gut microbiome

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease – Kyohei Nishino et al. – Journal of Gastroenterology

*Review: Host-microbiota interactions and adaptive immunity – Kathy D. McCoy et al. – Immunological Reviews (Special Issue: Microbiome-Immune System Interplay)

Animal experiments

Mouse: Commensal bacteria make GPCR ligands that mimic human signalling molecules – Louis J. Cohen et al. – Nature

Review: Exposure of livestock to GM feeds: Detectability and measurement – Anna Nadal et al. – Food and Chemical Toxicology

Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery -Eric R. Burrough et al. – Frontiers in Veterinary Science

Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome – Emily V. Lamoureux et al. – mSystems

Animal microbiome

Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont – Lin Cai et al. – Scientific Reports

Genomic diversification of giant enteric symbionts reflects host dietary lifestyles – David Kamanda Ngugi et al. – PNAS

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin – Daniel Medina et al. – Frontiers in Microbiology

Impact of egg disinfection of hatching eggs on the eggshell microbiome and bacterial load – R. Olsen et al. – Poultry Science

Plant, root and soil microbiome

Antioxidant and Antibacterial Activity of Organic Extracts of Roots of Glycyrrhiza Glabra Linn – Zafar Iqbal et al. – American Journal of Applied and Industrial Chemistry

Effect of red clover on the microbial transformation of phenanthrene and octadecane in the soil – A. V. Nazarov et al. – Eurasian Soil Science

Biogeography of plant-associated fungal symbionts in mountain ecosystems: A meta-analysis – Stephanie N. Kivlin et al. – Diversity and Distribution

Water and extremophile microbiome

Biodiversity analysis of the unique geothermal microbial ecosystem of the Blue Lagoon (Iceland) using next-generation sequencing (NGS) – Katarzyna A. Palinska et al. – Hydrobiologia

Impacts of tropospheric ozone exposure on peatland microbial consumers – Richard J. Payne et al. – Soil Biology and Biochemistry

Progress and perspectives in aquatic microbial ecology: highlights of the SAME 14, Uppsala, Sweden, 2015 – Eva S. Lindström & Paul A. del Giorgio – Aquatic Microbial Ecology

*Prevalence of β-lactamase genes in domestic washing machines and dishwashers and the impact of laundering processes on antibiotic resistant bacteria – Laura Rehberg et al. – Journal of Applied Microbiology

Built environment microbiome

A high-flow-rate impinger for the study of concentration, viability, metabolic activity, and ice nucleation activity of airborne bacteria – Tina Šantl-Temkiv et al. – Environmental Science & Technology

Phages and viruses

Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome – Matthew C. Johnson et al. – Journal of Structural Biology

Microbes in the news

Welcome Mat: Franklin art fair returns on Labor Day – Maureen Feighan – The Detroit News

Methane emissions tackled with gas-guzzling bacteria – Monash University – Science Daily

Altered Gut Bacteria Could Indicate Parkinson’s – Sylvia Booth Hubbard – News Max

*Health officials are warning Texans to stay out of Harvey floodwaters for a disturbing reason – Erin Brodwin – Business Insider

*Study shows nurses’ scrubs become contaminated with bacteria in hospitals – Medical Express

Cheaters take advantage – Irene Vacca – Nature Reviews Microbiology

Bacteria – Dot Wordsworth – The Spectator

New Oral Microbiome Study Could Provide Better Estimate of Time since Death – University of Tennessee

*Scientists Made Music From the Human Microbiome, and It’s Seriously Cool – Gears of Biz

How A Mother’s Letter Inspired A Scientist To Revolutionize Consumer Microbiome Testing – Afif Ghannoum – Forbes

Non-microbiology pick

Advocating for Diversity and Inclusion in Faculty Hiring – Darryl Yong and Sumun Pendakur – Notices of the AMS

August 29, 2017

A short list to digest today toward the end of the month.

Multi-site human microbiome

Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples – Clarke EL – American Journal of Respiratory and Critical Care Medicine

Human oral microbiome

Smoking May Lead to Marginal Bone Loss around Non-submerged Implant during Bone Healing by Altering Salivary Microbiome: A Prospective Study – Xiaobo Duan – Journal of Periodontology

Human skin microbiome

The mammalian skin microbiome – Ross, Ashley Anne – UWSpace

Human vaginal microbiome

Association between statin use, the vaginal microbiome, and Gardnerella vaginalis vaginolysin-mediated cytotoxicity – Abdelmaksoud AA – PLoS One

The cervico-vaginale microbiota in chlamydia trachomtais notified women: a case–control study at the sexually transmitted infection outpatient clinic in Amsterdam – Charlotte van der Veer – Virus Evolution

Human gut microbiome

Targeting the gut microbiota by dietary nutrients: a new avenue for human health – Li D – Critical Reviews in Food Science and Nutrition

Animal experiments

Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome – Lamoureux EV – mSystems

Plant, root, and soil microbiome

The Effects of Low Concentrations of Silver Nanoparticles on Wheat Growth, Seed Quality, and Soil Microbial Communities – Guangfu Liu – Water, Air, & Soil Pollution

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Microbiome Dynamics in a Shrimp Grow-out Pond with Possible Outbreak of Acute Hepatopancreatic Necrosis Disease – Wei-Yu Chen – Nature Scientific Reports 7

Microbes in the news

Science Is Showing How Gut Bacteria Affect The Brain, But Don’t Bother Taking Probiotics Yet – David DiSalvo – Forbes

Over 80% of airborne bacteria identical in Seoul, Beijing: report – Kim Da-sol – The Korea Herald

Ed’s non-microbiology picks 

Spontaneous fine-tuning to environment in many-species chemical reaction networks – Jordan M. Horowitz – PNAS

Bee-derived antibacterial peptide, defensin-1, promotes wound re-epithelialisation in vitro and in vivo – Marcela Bucekova – Nature Scientific Reports 7

Family Planning Funding Cuts and Teen Childbearing – Analisa Packham – Miami University