The new Microbiome Digest team

Microbiome Digest proudly presents: the New Microbiome Digest Team! From now on, Microbiome Digest will be taken over by a team of 21 enthusiastic scientist from all over the world.

I have tried to make this change as smoothly as possible, but I still anticipate some unanticipated SNAFU’s in the beginning. As we all need to adapt to this new style of publishing, there will probably be some irregularity in posting, some duplicate entries, or formatting issues. Or maybe you won’t notice anything at all!

Let’s give a warm welcome to the new Microbiome Digest team. Here is a short introduction to the new members (I am very short on time) – I will make a decent page with a better description in the near future.

Welcome on board!

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January 15, 2017

Microbes in Idiopathic Pulmonary Fibrosis, review on the female urinary microbiota, koalas with “wet bottom”, virus metagenomics of the Namib desert, biosignatures in fossils.


Microbiome Research Associate Job – Merck Research Laboratories – Cambridge, MA – Science Careers

Human urinary tract microbiome

* Review: The female urinary microbiota, urinary health and common urinary disorders – Linda Brubaker – Annals of Translational Medicine

Human respiratory microbiome

Host-Microbial Interactions in Idiopathic Pulmonary Fibrosis – Philip L Molyneaux – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The human gut microbiome as source of innovation for health: which physiological and therapeutic outcomes could we expect?: Human gut mibrobiome [SIC] as source of innovation for health – Joël Doré – Thérapie

In FrenchMicrobiote intestinal : qu’en attendre au plan physiologique et thérapeutique ? Le microbiote intestinal comme source d’innovation pour la santé – Joël Doré – Thérapie

Review: Seafood allergen-induced hypersensitivity at the microbiota-mucosal site: implications for prospective probiotic use in allergic response regulation – Linglin Fu – Critical Reviews in Food Science and Nutrition

Review: Impact Of Human Aging And Modern Lifestyle On Microbiota – Maria Gabriela Valle Gottlieb – Critical Reviews in Food Science and Nutrition

Review: Effects of environmental pollutants on gut microbiota – Yuanxiang Jin – Environmental Pollution

Animal experiments

Replacing corn with sorghum in the diet alters intestinal microbiota without altering chicken performance – N. S. Fagundes – Journal of Animal Physiology and Animal Nutrition

Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome – Francesco Rubino – The ISME Journal

Wolbachia Affects Reproduction and Population Dynamics of the Coffee Berry Borer (Hypothenemus hampei): Implications for Biological Control – Yobana A. Mariño – MDPI Insects

Neoagarotetraose protects mice against intense exercise induced fatigue damage by modulating gut microbial composition and function – Na Zhang – Molecular Nutrition & Food Research

Housing Systems Influence Gut Microbiota Composition of Sows but Not of Their Piglets – Tereza Kubasova – PLOS ONE

Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil (Anthonomus grandis) – Emiliano Ben Guerrero – Frontiers in Microbiology

Animal microbiome

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair Raymond Legione – bioRxiv

Plant, root, and soil microbiome

* Fossils: Carbonaceous biosignatures of diverse chemotrophic microbial communities from chert nodules of the Ediacaran Doushantuo Formation – Yuangao Qu – Precambrian Research

Plant, soil and microbial controls on grassland diversity restoration: A long-term, multi-site mesocosm experiment – Ellen L. Fry – Journal of Applied Ecology

Pyrosequencing reveals bacterial communities and enzyme activities differences after application of novel chiral insecticide Paichongding in aerobic soils – Jie Chen – Applied Soil Ecology

Cedar and bamboo plantations alter structure and diversity of the soil bacterial community from a hardwood forest in subtropical mountain – Yu-Te Lin – Applied Soil Ecology

The differentiation of soil bacterial communities along a precipitation and temperature gradient in the eastern Inner Mongolia steppe – Minjie Yao – CATENA

Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands – Julia Kyaschenko – The ISME Journal

Association between Grape Yeast Communities and the Vineyard Ecosystems – João Drumonde-Neves – PLOS ONE

Water microbiome

High growth potential and activity of 0.2 µm filterable bacteria habitually present in coastal seawater – Yumiko Obayashi – Biogeosciences Discuss

Chronic exposure effects of silver nanoparticles on stream microbial decomposer communities and ecosystem functions – Ahmed Tlili – Environmental Science & Technology

Waste and pollution microbiology

Global profiling of metabolite and lipid soluble microbial products in anaerobic wastewater reactor supernatant using UPLC/MSe – Phornpimon Tipthara – Journal of Proteome Research

Food microbiology

Rapid concentration detection and differentiation of bacteria in skimmed milk using surface enhanced Raman scattering mapping on 4-mercaptophenylboronic acid functionalized silver dendrites – Panxue Wang – Analytical and Bioanalytical Chemistry

Metagenomics and bioinformatics / Viruses and phages

Robust inference of genetic exchange communities from microbial genomes using TF-IDF – Yingnan Cong – Frontiers in Microbiology

Virome assembly and annotation: a surprise in the Namib Desert – Uljana Hesse – Frontiers in Microbiology

Metaviromes of Extracellular Soil Viruses along a Namib Desert Aridity Gradient – Olivier Zablocki – Genome Announcements

Metagenome Sequencing of Prokaryotic Microbiota Collected from Rivers in the Upper Amazon Basin – Célio Dias Santos-Júnior – Genome Announcements

Restoring the Duality between Principal Components of a Distance Matrix and Linear Combinations of Predictors, with Application to Studies of the Microbiome – Glen A. Satten – PLOS ONE

New approach for studying mobile genes using metagenomic analysis – Kazuyuki Ishihara – Oral Diseases


New insights into marine group III Euryarchaeota, from dark to light – Jose M Haro-Moreno – The ISME Journal


MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling – Kristin Burnum-Johnson – Analyst

An explanation of the Nagoya Protocol and Access and Benefit Sharing, and its implication for microbiology – David Smith – Microbiology

Microbes in the news

You’re probably showering way too often – Rafi Letzter – Business Insider

Viruses May Be Responsible For Life As We Know It – Ryan F. Mandelbaum – Gizmodo

Boost your intake of resistant starch to help your gut thrive – Leslie Beck – The Globe and Mail

We now know bacteria can communicate electrically, and we should be worried
They’re organised – David Nield – Science Alert

Proceed with caution: Autism Causes Update: The Gut-Brain Connection And How A Common Probiotic May Ease Symptoms – Lizette Borreli – Medical Daily

Study provides fundamental insights into functioning of microbiota and human-gut flora symbiosis – News Medical

Microbes on the market

Bristol-Myers Squibb and Enterome Announce Immuno-Oncology Collaboration Focused on Microbiome-Derived Biomarkers, Drug Targets and Bioactive Molecules – SAT Press Releases

Bik’s non-microbiology picks

The Physics of Everyday Life. Why popcorn pops and ducks don’t freeze when swimming in icy water. John Gribbin reviews “Storm in a Teacup” by Helen Czerski – Wall Street Journal

Lab stock photo fun – Grabbag

Here is an old draft I just found in a dusty corner of my blog – not much time today, but we can all need a laugh, so I will post it as-is.




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No, I have no idea where Patient #1 is – why ya asking? (Depositphotos)

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Stereotypical captions


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January 14, 2017

So it is technically already January 15 most countries, but I have been busy today preparing to transfer Microbiome Digest to an eager group of 20 new contributors. It takes a lot of time to hopefully be able to safe some time – if that makes sense.

My inbox is still full of new alerts, but here is what I have been able to “digest” so far. It’s already a lot!

General human microbiome

Navigating social and ethical challenges of biobanking for human microbiome research –
Kim H. Chuong – BMC Medical Ethics

Editorial: Influence of the microbiota on host physiology – moving beyond the gut
– Kim E. Barrett – The Journal of Physiology

Pregnancy and early life

* Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid – Diogo Antonio Tschoeke – BMC Medical Genomics

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota – Jasmine C. C. Davis – Scientific Reports

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

The Microbiome and Complement Activation A Mechanistic Model for Preterm Birth – Alexis B. Dunn – Biological Research for Nursing

Review: Asthma and the microbiome: defining the critical window in early life – Leah T. Stiemsma – Allergy, Asthma & Clinical Immunology

Human gut microbiome

Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Serum Trimethylamine N-oxide, Carnitine, Choline and Betaine in Relation to Colorectal Cancer Risk in the Alpha Tocopherol and Beta Carotene Study – Kristin A. Guertin – Cancer Epidemiology, Biomarkers & Prevention

Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection – Michael H. Woodwort – Journal of Clinical Microbiology

Editorial: Gut microbiota: implications for sports and exercise medicine – Owen Cronin – British Journal of Sports Medicine

Review/Addendum: Pathogen control at the intestinal mucosa – H2O2 to the rescue
Ulla G. Knaus – Gut Microbes

Editorial: Tune into the rhythm of your bugs – Purna Kashyap – Science Translational Medicine

Preview: Are Gut Microbes Responsible for Post-dieting Weight Rebound? – Julien Chilloux – Cell Metabolism

Review: Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease – Dawei Gong – Gastroenterology Research and Practice

Year in Review: Gut microbiota in 2016: A banner year for gut microbiota research – Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? – Vanina Guernier – BMC Infectious Diseases

Review: An expanding stage for commensal microbes in host immune regulation – Yan Shi – Cellular & Molecular Immunology

Perspective: Decoding host–microbiota communication in the gut – now we’re flying!
– Stephen J. Keely – The Journal of Physiology

Just based on the abstract, this appears a wild hypothesis potentially ignoring economic status, fiber consumption etc:  Latitude as a co-driver of human gut microbial diversity? – Emma Dikongué – Ideas that Push the Boundaries

Book: Gut Microbiome and Behavior, Volume 131 – John F. Cryan, Gerard Clarke – Elsevier

Animal experiments

Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice – Jaques Belik – Scientific Reports

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Year in review: Microbiome in 2016: T follicular helper cells and the gut microbiome in arthritis – Veena Taneja – Nature Reviews Rheumatology

Animal microbiome

Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms – Simon Bahrndorff – PLOS ONE

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) – Bettina Glasl – Coral Reefs

Symbiont-induced odorant binding proteins mediate insect host hematopoiesis – Joshua B Benoit – eLIFE

Drivers of variation in species impacts for a multi-host fungal disease of bats  –
Kate E. Langwig – Philosophical Transactions of the Royal Society B

Sponges: Evaluating the core microbiota in complex communities: A systematic investigation – Carmen Astudillo-Garcia – Environmental Microbiology

Plant, root, and soil microbiome

Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland – Haggai Wasserstrom – Scientific Reports

Phylogenetic relatedness, phenotypic similarity and plant–soil feedbacks – Connor R. Fitzpatrick

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Water microbiome

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China – Jingqiu Liao – Limnology and Oceanography

Built environment microbiome

Microbial diversity in different compartments of an aquaponics system – Zala Schmautz – Archives of Microbiology

Food microbiology

The influence of thiamine and riboflavin on various spoilage microorganisms commonly found in beer – Barry Hucker – The Journal of The Institue of Brewing

Waste and pollution microbiology

Microbial flora analysis for the degradation of beta-cypermethrin – Zhang Qi – Environmental Science and Pollution Research

Fungi (also see Animal Microbiome)

Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge – Neil A. R. Gow – Philosophical Transactions of the Royal Society B

Proteomics and metabolomics

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota – Aitor Blanco-Míguez – Database

PerspectiveProgress in the biology and analysis of short chain fatty acids – Roel J. Vonk – The Journal of Physiology

Bioinformatics and biostatistics

Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease – Mehrdad Yazdani – IEEE

Microscale Insight into Microbial Seed Banks – Kenneth J. Locey – Frontiers in Microbiology

* EMPeror: Bringing the Dynamic Microbiome to Life with Animations – Yoshiki Vázquez-Baeza – Cell Host & Microbe

Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities – Gongchao Jing – Scientific Reports

Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices – Hua X. – Human Heredity

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets – Xilin Xu – Biophysics Reports


Methodological flaws introduce strong bias into molecular analysis of microbial populations – N. Krakat – Journal of Applied Microbiology

Editorial: Microbial Nanoscopy: Breakthroughs, Challenges, and Opportunities – Yves F. Dufrêne – ACS Nano

More microbes

Asgard archaea illuminate the origin of eukaryotic cellular complexity – Katarzyna Zaremba-Niedzwiedzka – Nature

* Species-Independent Attraction to Biofilms through Electrical Signaling – Jacqueline Humphries – Cell

A bacterial global regulator forms a prion – Andy H. Yuan – Science

A periplasmic polymer curves Vibrio cholerae and promotes pathogenesis – Thomas M. Bartlett – Cell

Assembly of a nucleus-like structure during viral replication in bacteria – Vorrapon Chaikeeratisak – Science

Microbes in the news

Man’s best friend, bacteria’s worst enemy: dog sniffs out superbug in Canadian hospital – Ashifa Kassam – The Guardian

This article is not as bad as the title suggests but with photoshopped images:
Revealed: The millions of stomach-churning bacteria lurking in YOUR hair, skin, lungs, gut and mouth – and why – Mary Kekatos – Daily Mail

Video: Career profiles: Program Director at National Science Foundation Matthew Kane – American Society for Microbiology

A clear picture of bacteria: A new study has frozen bacteria extremely fast to gain a true-to-nature image of the internal and external structure – Science Daily

January 13, 2017

Nutrient acquisition by gut microbes, handling stress and gut microbiota changes in mice, evaluation of the MinION for microbiome studies.

Human gut microbiome

Structural basis for nutrient acquisition by dominant members of the human gut microbiota – Amy J. Glenwright – Nature

New light shed on functioning of human gut bacteria – Science Daily

Metabolic adaptation of colonic microbiota to galactooligosaccharides: a proof-of-concept-study – M. Mego – Alimentary Pharmacology and Therapeutics

Gut microbiota-dependent trimethylamine N-oxide in acute coronary syndromes: a prognostic marker for incident cardiovascular events beyond traditional risk factors – Xinmin S. Li, Slayman Obeid – European Heart Journal

Review: Basic Definitions and Concepts: Organization of the Gut Microbiome – Eamonn M.M. Quigley – Gastroenterology Clinics of North America

Animal experiments

Handling stress may confound murine gut microbiota studies – Cary R. Allen-Blevins – PeerJ

Water microbiome

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies – Laurence J. Clarke – Ecology and Evolution

Food microbiology

Cultivable microbiome of fresh white button mushrooms – W. Rossouw Letters in Applied Microbiology

Phages and viruses

Acquisition of Phage Sensitivity by Bacteria through Exchange of Phage Receptors – Elhanan Tzipilevich – Cell

For viral predators of bacteria, sensitivity can be contagiousNew modes of bacteriophage spread discovered – ScienceDaily


Evaluation of Oxford Nanopore MinION Sequencing for 16S rRNA Microbiome Characterization – Xiao Ma – bioRxiv

Lifetime of Phosphorescence from Nanoparticles Yields Accurate Measurement of Concentration of Oxygen in Microdroplets, Allowing One To Monitor the Metabolism of Bacteria – Michał Horka – Analytical Chemistry

Press: New type of monitoring provides information about the life of bacteria in microdroplets – Science Daily

Microbes in the news

Self-Experimenting Scientist Receives uBiome Grant to Investigate Consequences of Long-Term Antibiotic Use for Skin Conditions – PR Web

The art within Microbiology, and a coloring book – Chloe Schmidt – Frontiers Blog

Mapping the Microorganisms Behind Hospital-Borne Infections – Allison Bond – The Atlantic

Springfield Science Museum Explores the Human Microbiome – Business West

Researchers receive Moore Foundation grant to study the global ocean microbiome – Alan Flurry – University of Georgia

Scientists pave the way for enhanced detection and treatment of vascular graft infections – Science Daily

The Metabolome: The Missing Link that Binds the Microbiome with Human Health – Mike Milburn – GenEngNews

Proceed with caution: The Key to Reversing Autism May Be in the Microbiome – Emeran Mayer – Big Think

Microbes on the market

Carmel biotech firm scores major deal with pharmaceutical giant – Indianapolis Business Journal

Mawi DNA Technologies Launches ISWAB-Microbiome Sample Collection System – BusinessWire

Science, publishing, and career

Beware! Academics are getting reeled in by scam journals – The number of predatory publishers is skyrocketing – and they’re eager to pounce on unsuspecting scholars – Alex Gillis

January 12, 2017

uBiome blog

Losing Weight is the Most Popular New Year’s Resolution – Could Probiotics Help? – Julie Taylor – uBiome

Video: Young Microbiome Researchers: Celsius & Beyond – uBiome
For the uBiome team, working with other scientists is always rewarding, but we particularly enjoyed our recent collaboration with a team of researchers, many of whom were swamped by their lab coats and blue nitrile gloves.


Postdoctoral Research Fellow, Microbiology – California Academy of Sciences

Pregnancy and early life

* A molecular portrait of maternal sepsis from Byzantine Troy – Alison M Devault – eLIFE

The Generation R Study: design and cohort update 2017 – Marjolein N. Kooijman – European Journal of Epidemiology

Human oral microbiome

On the ecosystemic network of saliva in healthy young adults – Egija Zaura – The ISME Journal

Human gut microbiome

Seven brief reviews: Topical Issue of the Journal of Immunology: The Macro Influence of the Microbiome – Pamela J. Fink – The Journal of Immunology

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Animal experiments

Neuroblastoma causes alterations of the intestinal microbiome, gut hormones, inflammatory cytokines, and bile acid composition – Christoph Castellani – Pediatric Blood & Cancer

Routine assessment of the gut microbiome to promote preclinical research reproducibility and transparency – Hannah R Wardill – Gut

Animal microbiome

Postnatal changes in the relative abundance of intestinal Lactobacillus spp. in newborn calves – Tadashi Takino – Journal of Veterinary Medical Science

Population- and growth-related differences in helminthic fauna of finless porpoises (Neophocaena asiaeorientalis) in five Japanese populations – Akira Shiozaki – Journal of Veterinary Medical Science

Antifeedants Produced by Bacteria Associated with the Gut of the Pine Weevil Hylobius abietis – Karolin Axelsson – Microbial Ecology

Plant, root, and soil microbiome

Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel – Binu M. Tripathi – Microbial Ecology

Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil – Eoin Gunnigle – Scientific Report

Foliar application of the leaf-colonizing yeast Pseudozyma churashimaensis elicits systemic defense of pepper against bacterial and viral pathogens – Gahyung Lee – Scientific Reports

Response of microbial communities colonizing salt marsh plants rhizosphere to copper oxide nanoparticles contamination and its implications for phytoremediation processes – Joana P. Fernandes – Science of the Total Environment

Biodegradation of the veterinary antibiotics enrofloxacin and ceftiofur and associated microbial community dynamics – Diogo A.M. Alexandrino – Science of the Total Environment

Redox conditions and marine microbial community changes during the end-Ordovician mass extinction event – Justyna Smolarek – Global and Planetary Change

Use of plant growth promoting bacterial strains to improve Cytisus striatus and Lupinus luteus development for potential application in phytoremediation – María Balseiro-Romero – Science of the Total Environment

Response of microbial communities colonizing salt marsh plants rhizosphere to copper oxide nanoparticles contamination and its implications for phytoremediation processes -Joana P. Fernandes – Science of the Total Environment

Communication of Sedentary Plant-Parasitic Nematodes With Their Host Plants – T. Hewezi – Advances in Botanical Research

Book chapter: Application of Microbiology in Dryland Agriculture – Minakshi Grover – Innovations in Dryland Agriculture

Water and extremophile microbiome

Potential Activity of Subglacial Microbiota Transported to Anoxic River Delta Sediments – Karen A. Cameron – Microbial Ecology

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring – Laura Ward – The ISME Journal

Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics – Abraham G. Moller – PeerJ

Abundance of microorganisms and enzyme activity in the rapids-pool-benchland systems in natural Douliu River of China – Zhen Hong Wang – PeerJ Preprint

Distinct sensitivity of fungal freshwater guilds to water quality – Oliver Röhl – Mycological

Food microbiology

Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses – Jing Li – BMC Microbiology

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation – Peter R Sternes – bioRxiv

Waste and pollution microbiology

Microbial community structure in a full-scale anaerobic treatment plant during start-up and first year of operation revealed by high-throughput 16S rRNA gene amplicon sequencing – Else Marie Fykse – Bioresource Technology


* MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes – Wei Ma – Scientific Reports

Microbial ecology

Review: Where less may be more: how the rare biosphere pulls ecosystems strings – Alexandre Joussett – ISME Journal

Microbes in the news

Gut science is radically changing what we know of the human body – Pat Rich – University Affairs Canada

Renowned microbiology expert to visit West Florida. Claire Fraser will present, “The Human Gut Microbiome in Health and Disease” – SR Press Gazette

Microbiomes Move Standard Plate Count One Step Forward – Gregory Siragusa – Food Safety Tech

Researchers develop new compound to fight cytomegalovirus – EurekAlert

Eating red meat six times a week could increase chances of getting painful bowel disease – Daisy Dunne – Mirror

This looks intriguing: Microbiota and the masses: a love story – S. B. Divya – MacMillan

Microbes on the market

Gut microbiome profiling tests propelled by customer demand – Vijay Shankar – Nature Biotechnology

Bruker Announces Acquisition of CMO InVivo Biotech to Expand Molecular Biology, Microbiology and Pathology Consumables and Assay Business

Bik’s non-microbiology picks

UCSF Receives Historic Half-Billion-Dollar Donation – Lindsey Hoshaw – KQED

This is a tragic/comic read, but note that the original post contained some offending language, that was removed after protests on e.g. Twitter. The Rise and Fall of a Shrimp Biologist – David Scholnick – Scientific American

January 11, 2017

Vaginal microbial  communities associated with HIV acquisition or protection, evolution and function of the appendix, microbes and bird evolution, soil microbes followed for 17 years, and bone microbiome and cause-of-death of an 18th century child.

Faculty Position in Microbiome Research – National University of Singapore – Science Careers

Pregnancy and early life

The Role of Early Life Nutrition in the Establishment of Gastrointestinal Microbial Composition and Function – Erin C. Davis – Gut Microbes

Human vaginal microbiome

Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women – Christina Gosmann – Immunity

Diagnosis and microecological characteristics of aerobic vaginitis in outpatients based on preformed enzymes – Zhi-liang Wang – Taiwanese Journal of Obstetrics & Gynecology

Human respiratory microbiome

Review: The microbiome in mechanically ventilated patients – Yin, Yudong – Current Opinion in Infectious Diseases

Human gut microbiome

Morphological evolution of the mammalian cecum and cecal appendix – Heather F. Smith – Comptes Rendus Palevol

Exploring the Efficacy of Pooled Stools in Fecal Microbiota Transplantation for Microbiota-Associated Chronic Diseases – Abbas Kazerouni – PLOS ONE

Review: Role of Vitamin D in the Hygiene Hypothesis: The Interplay between Vitamin D, Vitamin D Receptors, Gut Microbiota, and Immune Response – Allison Clark – Frontiers in Immunology

Review: Bacterial Signaling to the Nervous System via Toxins and Metabolites – Nicole J. Yang – Journal of Molecular Biology

Animal experiments

Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior – Caleb Fischer – eLIFE

Gut Microbiota Mediates Protection Against Enteropathy Induced by Indomethacin – Xue Xiao – Scientific Reports

Faecal parameters as biomarkers of the equine hindgut microbial ecosystem under dietary change – P. Grimm – Animal

Characterisation of Early-Life Fecal Microbiota in Susceptible and Healthy Pigs to Post-Weaning Diarrhoea – Samir Dou – PLOS ONE

Animal microbiome

Metagenomic analysis of microbial community of a parasitoid wasp Megaphragma amalphitanum – A.V. Nedoluzhko – Genomics Data

* Review: Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history – Jessica K. Evans – Hormones and Behavior

Archaeology microbiome

The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing – Valeria D’Argenio – International Journal of Molecular Sciences

Plant, root, and soil microbiome

Phyllosphere Methylobacterium bacteria contain UVA-absorbing compounds – Shigenobu Yoshida – Journal of Photochemistry and Photobiology B: Biology

Major Crop Species Show Differential Balance between Root Morphological and Physiological Responses to Variable Phosphorus Supply – Yang Lyu – Frontiers in Plant Science

* Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change – Emma J. Sayer – Ecology and Evolution

Water and extremophile microbiome

Two microcrustaceans affect microbial and macroinvertebrate-driven litter breakdown – Sophie Chambord – Freshwater Biology

Biofilms Confer Resistance to Simulated Extra-terrestrial Geochemical Extremes – Adam H Stevens – bioRxiv Preprint

Bioinformatics, statistics, and metagenomics

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer – Aaron Weimann – mSystems

Structural zeros in high-dimensional data with applications to microbiome studies – Abhishek Kaul – Biostatistics

More microbiology

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response – Robert Heler – Molecular Cell

Press: Researchers Learn to Enhance Bacteria’s Ability to Form Genetic Memories – SciCasts

Microbes in the news
Meet Canada’s ‘poop lady’: “I got to know people up there very well over the years, said Girard, 28. – EurekAlert

A new year for our journal club! – Fiona Whelan – Human Microbiome Journal Club

Oral bacteria linked to preterm labor in Hawaiʻi – Desiree Uyeda – University of Hawai’i News

Mayo’s microbiome study targets diabetes – Brett Boese – Post Bulletin

MicrobEYEome: Liver Cancer Patients Have a Signature Microbiome – GastroEndo News

PresentationThe role of the microbiome in Porcine Reproductive & Respiratory Syndrome (PRRS) – Megan Niederwerder – YouTube

Based on the title this appears to be a good candidate for the “Overselling The Microbiome Award” by Jonathan Eisen: How Sexual Attraction Is Shaped by Gut Bacteria, Infectious Diseases, and Parasites – Kathleen McAuliffe – BigThink

Latest Dengue Update: Bacteria Strain That Stops Dengue Transmission In Mosquitoes Dies In Hot Environment – Minnow Blythe – Counsel Heal

Microbes on the market

Allergan (AGN) Enters Licensing Agreement with Assembly Biosciences (ASMB) to Obtain Worldwide Rights to GI Programs – StreetInsider

Ferring Partners with Intralytix to Develop Bacteriophage Treatments for Conditions Associated with the Microbiome and Drug-Resistant Bacteria – BusinessWire

La Roche-Posay Introduces Prebiotic Skincare Line – PR NewsWire

Indigo’s Preliminary Commercial Data Demonstrate Significant Yield Gains for Growers with Plant Microbiome Product – PR NewsWire

Bik’s non-microbiology picks

The Association of Hot Red Chili Pepper Consumption and Mortality: A Large Population-Based Cohort Study – Mustafa Chopan – PLOS ONE

January 10, 2017

A culture-based study of 2000 nasal microbiomes, eye metabolites, cardiorespiratory fitness in breast cancer survivors, Akkermansia from a python, chickpea rhizosphere, tobacco wilt suppression, plant rhizosphere mass spectrometry, phyloSkeleton.

Human nasal microbiome

Epidemiological and ecological modelling reveal diversity in microbial population structures from a cross-sectional community swabbing study – Abigail L Coughtrie – bioRxiv

Human eye microbiome

LC-MS-Based Metabolic Fingerprinting of Aqueous Humor – Karolina Pietrowska – Journal of Analytical Methods in Chemistry

Human vaginal microbiome

MS thesis: Metagenomic characterization of the vaginal microbiome – Keshini Devakandan – University of British Columbia

Human gut microbiome

Gut microbiota composition associated with alterations in cardiorespiratory fitness and psychosocial outcomes among breast cancer survivors – Jesseca A. Paulsen – Supportive Care in Cancer

SYN-004 (ribaxamase), an oral β-lactamase designed to protect the gut microbiome from the deleterious effects of certain intravenously administered β-lactam antibiotics, degrades ceftriaxone excreted into the intestine in Phase 2a clinical studies – John F. Kokai-Kun – Antimicrobial Agents Chemotherapy

Animal experiments

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis – Franziska Faber – PLOS Pathogens

Animal microbiome

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut – Janneke P. Ouwerkerk – Genome Announcements

Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and in eggs throughout development – Allison H. Kerwin – Environmental Microbiology

Plant, root, and soil microbiome

Competition between rhizobia under different environmental conditions affects the nodulation of a legume – Zhao Jun Ji – Systematic and Applied Microbiology

Combined pre-seed treatment with microbial inoculants and Mo nanoparticles changes composition of root exudates and rhizosphere microbiome structure of chickpea (Cicer arietinum L.) plants – E. N. Shcherbakova – Symbiosis

Interactions of soil particulate organic matter chemistry and microbial community composition mediating carbon mineralization in karst soils – Wei Xiao – Soil Biology and Biochemistry

Metabolic profiling of root exudates from two ecotypes of Sedum alfredii treated with Pb based on GC-MS – Qing Luo – Scientific Reports

Effects of Wetland Vegetation on Soil Microbial Composition: A Case Study in Tumen River Basin, Northeast China– Qin Lei – Chin. Geogra. Sci

Microbial communities in pyrene amended soil–compost mixture and fertilized soil – Iris K. U. Adam – AMB Express

Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi – Maja Hilber-Bodmer – BMC Microbiology

Tobacco bacterial wilt suppression with biochar soil addition associates to improved soil physiochemical properties and increased rhizosphere bacteria abundance – Chengsheng Zhang – Applied Soil Ecology

Editorial: Microbial community ecology: Function over phylogeny – Sean M. Gibbons – Nature Ecology & Evolution

Review: Elucidating rhizosphere processes by mass spectrometry – A review – Ariana Rugova – Analytica Chimica Acta

Water and extremophile microbiome

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments – Marc Mußmann – The ISME Journal

Food microbiology

ReviewAn Integrated View of the Effects of Wine Polyphenols and Their Relevant Metabolites on Gut and Host Health – Carolina Cueva – Molecules

Microbiological quality of Brazilian UHT milk: Identification and spoilage potential of spore-forming bacteria – Claudia L O Pinto – International Journal of Dairy Technology

Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages – Digar Singh – Trends in Food Science & Technology

Source tracking of prokaryotic communities in fermented grain of Chinese strong-flavor liquor – Xueshan Wang – International Journal of Food Microbiology


phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics – Lionel Guy – Bioinformatics

Microbes in the news

Hyperthermophiles and Cryophiles: The World’s Most Extreme Organisms – Priya Amin – Harvard Science Review

Bik’s non-microbiology picks

Responses of Human Neonates to Highly Diluted Odorants from Sweat – Helene M. Loos – Journal of Chemical Ecology

January 9, 2017


Reminder: Microbiome meetup (SF Bay Area) – Tools & Techniques for analysis
by SF Bay Area Microbiome Meetup – January 31, 2016, Illumina, San Francisco. Free.

Human gut microbiome

Water activity does not shape the microbiota in the human colon – Doris Vandeputte – Gut

ReviewThe thyroid, the eyes and the gut: a possible connection – D. Covelli – Endocrinological Investigation

Review: Role of intestinal microbiota and metabolites on gut homeostasis and human diseases – Lan Lin – BMC Immunology

Review: Gut microbiota and colorectal cancer – R. Gao – European Journal of Clinical Microbiology & Infectious Diseases

Review: How the Gut Affects Bone Metabolism – Marie-Hélène Lafage Proust – Joint Bone Spine

The role of gut microbiota in health and disease: In vitro modeling of host-microbe interactions at the aerobe-anaerobe interphase of the human gut – Julius Z.H. von Martels – Anaerobe

Animal experiments

Replacing corn with sorghum in the diet alters intestinal microbiota without altering chicken performance – N. S. Fagundes – Journal of Animal Physiology and Animal Nutrition

Quantitative analyses of the bacterial microbiota of rearing environment, tilapia and common carp cultured in earthen ponds and inhibitory activity of its lactic acid bacteria on fish spoilage and pathogenic bacteria – Pierre Marie Kaktcham – World Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado – Ademir Sergio Ferreira de Araujo – Antonie van Leeuwenhoek

Soil microbial communities are shaped by vegetation type and park age in cities under cold climate – Nan Hui – Environmental Microbiology

Water and extremophile microbiome

The effect of coagulants and antiscalants discharged with seawater desalination brines on coastal microbial communities: A laboratory and in situ study from the southeastern Mediterranean – Natalia Belkin – Water Research

DNA metabarcoding reveals that 200 μm size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes – Lemian Liu – Molecular Ecology Resources

Water metagenomic analysis reveals low bacterial diversity and the presence of antimicrobial residues and resistance genes in a river containing wastewater from backyard aquacultures in the Mekong Delta, Vietnam – Tatsuya Nakayama –

Waste and pollution research

Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure – Jo De Vrieze – Water Research


The rumen microbial metaproteome as revealed by SDS-PAGE – Timothy J. Snelling – BMC Microbiology

Microbes in the news

Deadly, Invisible Bacteria Melioidosis Spreads In Top End Monsoon – Cayla Dengate – The Huffington Post

I’m Fasting For Science: Will It Help Tame My Multiple Sclerosis? – Brandie Jefferson – NPR

Help wanted for Microbiome Digest

Quick update on January 10: Thank you for an inbox full of applications! I will try to write back to each of you personally and set up a rotating publication scheme. I hope I have time to set something up over the upcoming weekend!

I’ve been running my Microbiome Digest blog almost continuously for 2.5 years. And it will come as no surprise that this has been slowly taking more and more of my time. So today’s post is about realizing that I will be needing some help to keep on running it.

The first Microbiome Digest post was on May 21, 2014. Click on the link to see how short it is, and compare that with the posts from the last couple of days. It took me more than 4 hours to prepare Thursday’s post!

The microbiome field has been growing a lot over the past few years, and I get more and more alerts and numbers of new papers to go through every day. Just look at the steady increase of the number of papers in the microbiome field on Pubmed. There is no sign that it’s slowing down anytime soon!

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Before Microbiome Digest was online, I had already been sending out nearly daily literature update emails to my Stanford coworkers for a couple of months. So in the past 3 years, I have been going through my alerts and preparing posts almost every day. After long days of lab work or data analysis. When I was writing a grant proposal. In the weekends. While traveling for work. On vacations. When I was sick. After the funeral of my sister. After burying my cat. At 1 AM. In hotel rooms and at airports, but usually at home.

Preparing the daily Digest has gradually taken away all my free time. I have not watched TV in years. I have no idea what Game of Thrones is. Or West World. No time. The Digest always came first. On some days, it was easy. Just 30 papers to scan. On others, it was hundreds. There were days when I cried to see 10 new long Google Scholar alerts come in. But I always kept on going, because I did not want to disappoint my readers. However, the amount of work is starting to take away my 8 hours of sleep, and the past months have been very tough, and I’ve decided that I need to delegate some work to someone else.

So: I am looking for a couple of people who can help me run my blog. It would involve going through the alerts I have set up, selecting interesting papers, checking if they have already been posted in the previous days, sorting them in categories, getting the links to the papers, and write and publish a blog post via Wordpress. Ideally, we would have enough people in our team so we could all take turns, only have to do this once a week, with the flexibility to switch in case of the occasional travel or illness. I usually do the work at night to prepare for the next morning, but it could also be done in the early morning. As long as we can continue to post every day around 9am Pacific time.

The ideal person to do this job would be / have:

  • Graduate student or postdoc
  • Working on human, animal, plant, or environmental microbiome
  • Can commit to a block of 2-4 hours on a set day of the week
  • Experience using PubMed and Google Scholar
  • Reliable person with reliable access to computer and internet
  • Interest in science writing/science communication

Just to make sure, this is a voluntary, unpaid position. But it will help you to stay on top of the microbiome literature, never run out of papers to contribute for Journal Club, broaden your network, and expand your resume and experience.

Please contact me at my gmail address (see below), using “Microbiome Digest Help” as the subject line – the ability to follow instructions will be part of the selection process 😀   – and only contact me if you can seriously commit to at least one night per week. Just a one-paragraph description of who you are, what your topic of research is, and why you would love to be part of this new team is enough. No need to send a resume or CV. Thanks!


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