February 14, 2018

The role of saliva in structuring human oral bacterial communities, effects of permafrost thaw on methanogenic communities, and articles on the microbiomes of termites, burying beetles, honey bees, and mosquitoes.

Human oral microbiome

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow – Diana M Proctor – Nature Communications

Human vaginal microbiome

To ‘douche’ or not to ‘douche’: hygiene habits may have detrimental effects on vaginal microbiota – Erdogan Aslan – Journal of Obstetrics and Gynaecology

Human gut microbiome

Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota – Carolina Serena – The ISME Journal

Infection and Microbiome: Impact of Tuberculosis on Human Gut Microbiome of Indian Cohort – Utkarsh Sood – Indian Journal of Microbiology

Comparative metaproteomics analysis shows altered fecal microbiota signatures in patients with major depressive disorder – Zhi Chen – NeuroReport

Animal experiments

Protective effect of Group B Streptococcus type-III polysaccharide conjugates against maternal colonization, ascending infection and neonatal transmission in rodent models – Emiliano Chiarot – Scientific Reports

Animal microbiome

Pre-print: Axenic Aedes aegypti develop without live bacteria, but exhibit delayed development and reduced oviposition – Maria A Correa – bioRxiv

Two novel strains of Torulaspora delbrueckii isolated from the honey bee gut microbiome and their use in honey fermentation – Joseph P Barry – bioRxiv

Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang – Ecology and Evolution

Rampant Host Switching Shaped the Termite Gut Microbiome – Thomas Bourguignon – Current Biology

Plant, root, and soil microbiome

Melanization of mycorrhizal fungal necromass structures microbial decomposer communities – Christopher W Fernandez – Journal of Ecology

Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence – Andreas Hagenbo – Journal of Ecology

Mycorrhizal symbioses influence the trophic structure of the Serengeti – Bo Maxwell Stevens – Journal of Ecology

The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome – M A Cregger – Microbiome

Water and extremophile microbiome

Pre-print: Transgenerational inheritance of shuffled symbiont communities in the coral Montipora digitata – Kate Quigley – bioRxiv

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes – Shiping Wei – Extremophiles

Food microbiology

Dynamic correlations between microbiota succession and flavor development involved in the ripening of Kazak artisanal cheese – Xiaoji Zheng – Food Research International

Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study – Daleniece Higgins – Food Research International

Phages and viruses

The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain) – Vicente Pérez-Brocal – PLOS ONE

More microbes

Lactobacillus plantarum lipoteichoic acid inhibits biofilm formation of Streptococcus mutans – Ki Bum Ahn – PLOS ONE

Microbes in the news

In soil-dwelling bacteria, scientists find a new weapon to fight drug-resistant superbugs – Melissa Healy – Los Angeles Times

Interdisciplinary approach yields new insights into human evolution – Liz Entman – Vanderbilt University News

Viruses and Bacteria Travel Along a High-Altitude Superhighway – Dave Roos – Seeker

Science, career, and publishing

Pre-print: The impact on authors and editors of introducing Data Availability Statements at Nature journals – Rebecca Grant – bioRxiv


February 13, 2018

The gut microbiome of honey bee workers, a review of “Foodomics” approaches to studying digestion and bioactivity, and a new genome sequence for a bacterium isolated from a cell phone screen.

Human gut microbiome

Review: Causal effects of the microbiota on immune-mediated diseases – June L Round – Science Immunology

Possible correlation between gut microbiota and immunity among healthy middle-aged and elderly people in southwest China – Xi Shen – Gut Pathogens

Animal experiments

Pre-print: Clostridium difficile alters the structure and metabolism of distinct cecal microbiomes during initial infection to promote sustained colonization – Matthew L Jenior – bioRxiv

Pre-print: Microbiota metabolic product deoxycholic acid controls chicken necrotic enteritis – Hong Wang – bioRxiv

Effects of Bentonite Bgp35b-p on the Gut Microbiota of Mice Fed a High-Fat Diet – Eun-Sook Lee – Science of Food and Agriculture

Animal microbiome

The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science

Bacterial density rather than diversity correlates with hatching success across different avian species – Juan Manuel Peralta-Sánchez – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Influence of metal contamination in soil on metabolic profiles of Miscanthus x giganteus belowground parts and associated bacterial communities – Hoang Nam Pham – Applied Soil Ecology

Pre-print: In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana – Claudia Bartoli – bioRxiv

Effects of Using Arbuscular Mycorrhizal Fungi to Alleviate Drought Stress on the Physiological Traits and Essential Oil Yield of Fennel – Sedigheh Gheisari Zardak – Rhizosphere

Water and extremophile microbiome

Pre-print: Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities – Elena Butaitė – bioRxiv

Bacteria from Coral Ecosystem of Kiltan Island, Lakshadweep: Resource for Hydrolytic Enzymes – L Ramlath – International Journal of Cell Science and Biotechnology

Built environment

Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone – Praveen Rahi – International Journal of Systematic and Evolutionary Microbiology

Food microbiology

Review: The role of Foodomics to understand the digestion/bioactivity relationship of food – Grégory Pimentel – Current Opinion in Food Science

Phages and viruses

Virus-mediated transfer of nitrogen from heterotrophic bacteria to phytoplankton – Emma J Shelford – Biogeosciences

Small RNA-omics for virome reconstruction and antiviral defense characterization in mixed infections of cultivated Solanum plants – Silvia Turco – Molecular Plant-Microbe Interactions


UPLC-QTOF-MS metabolomics analysis revealed the contributions of metabolites to the pathogenesis of Rhizoctonia solani strain AG-1-IA – Wenjin Hu – PLOS ONE

Microbes in the news

New imaging technique reveals how dragonfly wings tear bacteria apart – Alayna Hansen – New Atlas

Exploring the microbiome of an ocean bacteria – Kyle Frischkorn – Phys.Org

Microbes on the market

Rebiotix Develops Microbiome Health Index™ to Identify Indicators for Microbiome Restoration – PR Newswire

Bristol-Myers taps Sirenas for ‘global microbiome’ drug discovery – Amirah Al Idrus – FierceBiotech

Givaudan, Unilever target the microbiome – Marc S Reisch – Chemical & Engineering News

February 12, 2018

A rich Digest to start your work week. Highlights include a review in Lancet cautionary about precision nutrition, an NIH metagenome FTP site, and a sampling of songbirds that reveals high prevalence of antibiotic resistant bacteria.


Intellectual Property x The Microbiome – SF Bay Area Microbiome Meetup

General microbiology

Expanding our Understanding of the Role of the Microbiome in Health and Disease – Rob Knight – Archives of Medical Research

* NIH Metagnome FTP site

* The Ecosystem Services of Animal Microbiomes – E.A. McKenney et al. – Molecular Ecology

Preprint: Experimental Evolution of Cell Shape in Bacteria – Paul Richard Yulo et al. – bioRxiv

Human skin microbiome

In vitro: Yeasts from skin colonization are able to cross the acellular dermal matrix – Isabele Carrilho Jarros et al. – Microbial Pathogenesis

Human vaginal microbiome

Review: Immunology of the Uterine and Vaginal Mucosae – Jordan Z. Zhou et al. – Trends in Immunology

Human gut microbiome

The Role of Diet in the Treatment of Irritable Bowel Syndrome : A Systematic Review – Rajdeep Singh et al. – Gastroenterology Clinics of North America

Review: Metabolic Surgery : Weight Loss, Diabetes, and Beyond – Manan Pareek et al. – Journal of the American College of Cardiology

Review: Environmental Noise and the Cardiovascular System – Thomas Münzel et al. – Journal of the American College of Cardiology

The effects of synbiotic supplementation on insulin resistance/sensitivity, lipid profile and total antioxidant capacity in women with gestational diabetes mellitus: a randomized double blind placebo controlled clinical trial – Zohoor Nabhani et al. – Diabetes Research and Clinical Practice

* Precision nutrition for prevention and management of type 2 diabetes – Dong D Wang and Frank B Hu – The Lancet Diabetes & Endocrinology

The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids – Cholsoon Jang et al. – Cell Metabolism

Review: Therapeutic implications of the gastrointestinal microbiome – Purna C Kayshap and Eamonn MM Quigley – Current Opinion in Pharmacology

Risk factors for Clostridium difficile infection in intestinal transplant recipients during the first year post transplant – Luis Guzman et al. – Transplant Infectious Disease


Review: Advances in computational metabolomics and databases deepen the understanding of metabolisms – Hiroshi Tsugawa – Current Opinion in Biotechnology

Animal experiments

Rat: Onion quercetin monoglycosides alter microbial activity and increase antioxidant capacity – Katarzyna Grzelak-Błaszczyk et al. – The Journal of Nutritional Biochemistry

Preview: Cultivating a Relationship with Gut Bacteria – Catherine E. Schretter and Sarkis K. Mazmanian – Cell Metabolism

Effect of two seaweed polysaccharides on intestinal microbiota in mice evaluated by illumina PE250 sequencing – Zhongshan Zhang et al. – International Journal of Biological Macromolecules

Green Tea Polyphenols Modulate Colonic Microbiota Diversity and Lipid Metabolism in High-Fat Diet Treated HFA Mice – Li Wang et al. – Journal of Food Science

Animal microbiome

* Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments – Diana L. Carter et al. – Science of The Total Environment

Effects of chlorogenic acids-enriched extract from Eucommia ulmoides leaves on growth performance, stress response, antioxidant status and meat quality of lambs subjected or not to transport stress – H.W. Liu et al. – Animal Feed Science and Technology

Characterisation of Bergeyella spp. isolated from the nasal cavities of piglets – M. Lorenzo de Arriba et al. – The Veterinary Journal

Horse: The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins – L.E. Peachey et al. – International Journal for Parasitology

The effects singular or combined administration of fermentable fiber and probiotic on mucosal immune parameters, digestive enzyme activity, gut microbiota and growth performance of Caspian white fish (Rutilus frisii kutum) fingerlings – Ali Taheri Mirghaed et al. – Fish & Shellfish Immunology

Diagnostics and Treatments in Chronic Diarrhea and Weight Loss in Horses – Olimpo Oliver-Espinosa – Veterinary Clinics: Equine Practice

Plant, root and soil microbiome

Diversifying crop rotation increased metabolic soil diversity and activity of the microbial community – Luciana D’Acunto et al. – Agriculture, Ecosystems & Environment

The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome – Franck Stefani et al. – Scientific Reports

Water and extremophile microbiome

Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis – Renxin Zhao et al. – Water Research

Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH – Raquel Quatrini and D Barrie Johnson – Current Opinion in Microbiology

Effect of heat shock on hot water plumbing microbiota and Legionella pneumophila control – Pan Ji et al. – Microbiome

Food microbiology

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts et al. – Food Microbiology

Modelling the growth of Listeria monocytogenes in Mediterranean fish species from aquaculture production – Araceli Bolívar et al. – International Journal of Food Microbiology

Prebiotic in fruit juice: processing challenges, advances, and perspectives – Thatyane Vidal Fonteles and Sueli Rodrigues – Current Opinion in Food Science


Multi-omics approach to elucidate the gut microbiota activity. Metaproteomics and metagenomics connection – Maria Guirro et al. – Electrophoresis

Microbes in the news

Can Your Gut Protect You Against Cancer? – Michelle Schoffro Cook – Care2

Millions of Mosquitoes to Be Released in Florida for Good Cause – Inside Edition

Using Special UV Light in Public Spaces Could Kill Flu Viruses, Bacteria – Jakob Nielson – Apex Tribune


February 11, 2018

General microbiome

How the microbiome challenges our concept of self – Tobias Rees, PloS Biology

Human gut microbiome

Inflammatory bowel disease and Clostridium difficile infection: contrasting views of international clinical professionals – Andreas Stallmach, Zeitschrift für Gastroenterologie

Digestibility of sulfated polysaccharide from the brown seaweed Ascophyllum nodosum and its effect on the human gut microbiota in vitro – Ligen Chen, International Journal of Biological Macromolecules

Microbiome-based mechanisms hypothesized to initiate obesity-associated rheumatoid arthritis – Y. Luo, Obesity Reviews

Tissue macrophages as mediators of a healthy relationship with gut commensal microbiota – Brenda Naemi Nakagaki, Cellular Immunology

Fecal microbiota transplantation for recurrent Clostridium difficile infection in a patient with ulcerative colitis – Kosaku Nanki, Intestinal Research

Efficacy and safety of the adalimumab biosimilar Exemptia as induction therapy in moderate-to-severe ulcerative colitis – Vandana Midha, Intestinal Research

Sensing Bacterial-Induced DNA Damaging Effects via Natural Killer Group 2 Member D Immune Receptor: From Dysbiosis to Autoimmunity and Carcinogenesis – J. Luis Espinoza, Frontiers in Immunology

Environmental Exposures and Neuropsychiatric Disorders: What Role Does the Gut–Immune–Brain Axis Play? – Shannon Delaney, Current Environmental Health Reports

Human nearly-sterile sites

Identification and Characterization of Blood and Neutrophil-Associated Microbiomes in Patients with Severe Acute Pancreatitis Using Next-Generation Sequencing – Qiurong Li, Frontiers in Cellular and Infectious Microbiology

Animal experiments

Effects of levan-type fructan on growth performance, nutrient digestibility, diarrhoea scores, faecal shedding of total lactic acid bacteria and coliform bacteria, and faecal gas emission in weaning pigs – Xin Jian Lei, Journal of the Science of Food and Agriculture

Dietary proline supplementation alters colonic luminal microbiota and bacterial metabolite composition between days 45 and 70 of pregnancy in Huanjiang mini-pigs – Yujiao Ji, Journal of Animal Science and Biotechnology

Effects of the Artificial Sweetener Neotame on the Gut Microbiome and Fecal Metabolites in Mice – Liang Chi, Molecules

Animal microbiomes

Functional Transcripts Indicate Phylogenetically Diverse Active Ammonia-Scavenging Microbiota in Sympatric Sponges – Guofang Feng, Marine Biotechnology

Community structure, dispersal ability and functional profiling of microbiome existing in fat body and ovary of the brown planthopper, Nilaparvata lugens – Jian-Hua Zhang, Insect Science

Plant, root, and soil microbiome

Influence of biochar aged in acidic soil on ecosystem engineers and two tropical agricultural plants – Ihuoma N. Anyanwu, Ecotoxicology and Environmental Safety

Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems –  Juan Ling, Frontiers in Microbiology

Dibutyl phthalate alters the metabolic pathways of microbes in black soils – Weihui Xu, Scientific Reports

Native soils with their microbiotas elicit a state of alert in tomato plants – Matteo Chialva, New Phytologist

Water and extremophile microbiome

A probabilistic approach to assess antibiotic resistance development risks in environmental compartments and its application to an intensive aquaculture production scenario – Andreu Rico, Environmental Pollution

Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific) – Julia Endresen Storesund, Antonie van Leeuwenhoek

Enhancing methane production from lignocellulosic biomass by combined steam-explosion pretreatment and bioaugmentation with cellulolytic bacterium Caldicellulosiruptor bescii – Daniel Girma Mulat, Biotechnology for Biofuels

Microbial ecology

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle – K. Dimitri Kits, Nature Letters

Microbes in the news

Safety blunders expose lab staff to potentially lethal diseases in UK – The Guardian

This UV Lamp Could Prevent the Flu Virus From Spreading in Public Places –  Amanda Macmillan, Time

February 10, 2018

Check out the Environmental Microbiology * The New Microscopy themed issue from
Events and jobs from Current Opinion in Microbiology! Other highlights include bioinformatic and wet lab techniques, including fecal water preparation for metabolomics and SMRT, as well as a new version of Kraken with k-mer coverage (KrakenHLL)!

Jobs and events
PhD scholarships in Microbiome Synthetic Biology – Danmarks Tekniske Universitet

Human respiratory microbiome
Dysbiosis of inferior turbinate microbiota is associated with high total IgE levels in allergic rhinitis patients – Dong-Wook Hyun – Infection and Immunity

Human skin microbiome
Epidermal lipid composition, barrier integrity and eczematous inflammation are associated with skin microbiome configuration  – Hansjörg Baurecht – Journal of Allergy and Clinical Immunology

Human oral microbiome
Presence of archaea and selected bacteria in infected root canal system – Ewa Brzezińska-Błaszczyk – Canadian Journal of Microbiology

Human gut microbiome
ReviewUnderstanding the Microbiome: Emerging Biomarkers for Exploiting the Microbiota for Personalized Medicine against Cancer – Meenakshi Rajpoot – Seminars in Cancer Biology

Animal microbiome
Exploring virulence of new and less studied species of Metarhizium spp. from Brazil for two-spotted spider mite control – Thiago Castro – Experimental and Applied Acarology

Plant, root, and soil microbiome
Soil metagenome-derived 3-hydroxypalmitic acid methyl ester hydrolases suppress extracellular polysaccharide production in Ralstonia solanacearum – Myung Hwan Lee – Journal of Biotechnology

Effects of rhizosphere interactions of grass interspecies on the soil microbial properties during the natural succession in the Loess Plateau – Chao Zhang – European Journal of Soil Biology

Degradation of polycyclic aromatic hydrocarbons in soil mesocosms by microbial/plant bioaugmentation: Performance and mechanism – Fan-xin Kong – Chemosphere

The influence of tree species on soil properties and microbial communities following afforestation of abandoned land in northeast China – Na Yang – European Journal of Soil Biology

Diversity of the bacterial microbiome in the roots of four Saccharum species: S. spontaneum, S. robustum, S. barberi, and S. officinarum – Meng Dong – Frontiers in Microbiology

Water and extremophile microbiome
Current Opinion in Microbiology has a themed issue called Environmental Microbiology * The New Microscopy with many articles of interest, some including:

First Investigation of Microbial Community Composition in the Bridge (Gadeok Channel) between the Jinhae-Masan Bay and the South Sea of Korea – Jiyoung Lee – Ocean Science Journal

The effect of temperature on the microbial communities of peak biogas production in batch biogas reactors – Guangliang Tian – Renewable Energy

The Effects of Antibiotics on Microbial Community Composition in an Estuary Reservoir during Spring and Summer Seasons – Zheng Xu – Water

Built environment
Review: Advances in concrete materials for sewer systems affected by microbial induced concrete corrosion: A review – Cyrill Grengg – Water Research

Microbial interactions
Comparative study on nutrient depletion-induced lipidome adaptations in Staphylococcus haemolyticus and Staphylococcus epidermidis – Yu Luo – Scientific Reports

The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp – Hung-Yu Liao – Journal of Hazardous Materials

Probiotics / prebiotics / antibiotics
Evolutionary trajectories to amoxicillin-clavulanic acid resistance in Escherichia coli are affected by growth media – Alasdair TM Hubbard – biorXiv

ComPAS: Community Preserving Sampling for Streaming Graphs – Sandipan Sikdar – arXiv

KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts – Florian P Breitwieser – bioRxiv

Efficient non-cytotoxic fluorescent staining of halophiles – Ivan Maslov – Scientific Reports

Metabonomic Evaluation of Fecal Water Preparation Methods: The Effects of Ultracentrifugation – Sandi Yen – Current Metabolomics

SMRT-Cappable-seq reveals complex operon variants in bacteria – Bo Yan – bioRxiv

Microbes in the news
Are Hand Dryers Actually Full of Bacteria? A Viral Photo Doesn’t Tell the Whole Story – Maggie Astor – New York Times

Bacteria-infected mosquitoes might be good thing for Miami – Jennifer Kay – ABC News
Miami releases bacteria-infected mosquitoes to help fight Zika virus – KGUN9

UV Light That Is Safe for Humans but Bad for Bacteria and Viruses – GEN News

Stanford Global Health awards seed funding to nine projects – Stanford Medicine News Center

Microbes on the market
Seres Therapeutics Inc. (MCRB) Settles Into New 52-Week Low on February 08 Session – Equities.com

Tiffany’s other picks
Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain – Sylvie Janssens – mSystems


February 9, 2018

Transcriptomics in wildlife, skin microbiota, phages and a lot more for today’s digest!

Events and jobs


Assistant Professor in Metagenomics and Bioinformatics, tenure-track position – Kansas State University – Manhattan, USA

General microbiome

Review: Linking the Gut Microbiota to Bone Health in Anorexia Nervosa – NC Aurigemma – Current Osteoporosis Reports

Research Agenda for Microbiome Based Research for Multidrug-resistant Organism Prevention in the Veterans Health Administration System – AE Kates – Infection Control & Hospital Epidemiology

Tumour-associated and non-tumour-associated microbiota: Addendum – B Flemer – Gut Microbes

Preprint: An Escherichia coli nitrogen starvation response is important for mutualistic coexistence with Rhodopseudomonas palustris – AL McCully – bioRxiv


Human skin microbiome

Nature-oriented daycare diversifies skin microbiota in children – no robust association with allergies. – J Lehtimäki – Pediatric Allergy and Immunology

Epidermal lipid composition, barrier integrity and eczematous inflammation are associated with skin microbiome configuration – H Baurecht – The Journal of Allergy & Clinical Immunology


Human gut microbiome

Review: Pathophysiology of Functional Gastrointestinal Disorders: A Holistic Overview – G Holtmann – Karger

Preprint:  Stronger connectivity of the resident gut microbiome lends resistance to invading bacteria – CM Herren – bioRxiv

Animal experiments 

Enteric Immunity : Happy Gut, Healthy Animal – CCL Chase – Veterinary Clinics of North America: Food Animal Practice

Influence of changes in the intestinal microflora on the immune function in mice – S Kishida – Journal of Veterinary Medical Science

In Vivo Assessment of Resistant Starch Degradation by the Caecal Microbiota of Mice Using RNA-Based Stable Isotope Probing—A Proof-of-Principle Study – E Herrmann – Nutrients

Animal microbiome 

A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations – LJ Campbell – Molecular Ecology

The bacterial community associated with the sheep gastrointestinal nematode parasite Haemonchus contortus – G Sinnathamby – PLoS One

Mucus glycosylation and immunity, and bacterial microbiota associated to the skin of experimentally ulcered gilthead seabream (Sparus aurata). – ST Tapia-Paniagua – Fish & Shellfish Immunology

Modulation of gut microbiota by dietary supplementation with tuna oil and algae oil alleviates the effects of D-galactose-induced ageing – H Zhang – Applied Microbiology and Biotechnology

Probiotic treatment during neonatal age provides optimal protection against experimental asthma through the modulation of microbiota and T cells: Neonatal exposure to probiotics prevents asthma – CFCG Nunes – International Immunology

Plant, root and soil microbiome

Activating biochar by manipulating the bacterial and fungal microbiome through pre-conditioning. – AK Jaiswal – New Phytologist


Food microbiology

Growth potential of Listeria monocytogenes in twelve different types of RTE salads: impact of food matrix, storage temperature and shelf life – M Ziegler – bioRxiv

Phages and viruses

Lysogeny is prevalent and widely distributed in the murine gut microbiota – M-S Kim – The ISME Journal

Preprint: A T7 phage factor required for managing RpoS in Escherichia coli  – A Tabib-Salazar – bioRxiv

Preprint: Genotypic and phenotypic diversity within the neonatal HSV-2 population – LN Akhtar – bioRxiv


Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis – R Khan – PLoS One

Microbes in the news

Reality check: Are hand dryers in public bathrooms full of bacteria and fungi? – Global News

Consider skipping orange juice in the morning  – Channel NewsAsia

‘Dozens of bacteria:’ After 2 days, snow is no longer safe to eat, study reveals  – Fox6 Now

Termites’ unique gut ‘factory’ key to global domination – Phys.org

Bacteria persist as stowaways – Innovations Report

Genomic Analysis Finds Hospital Plumbing Harbors Antibiotic Resistant Bacteria – Genome Web

Skin microbiome announces agenda – Cosmeticsdesign.com



February 8, 2018

Many interesting articles today: the geographical location of habitat has a stronger impact on the fecal microbiome of lemurs than sex, age, or species;  the mechanism for pathobiont-dependent inflammatory bowel disease involves microbiota reactive T cells; highly active antiretroviral therapy can restore gut microbiome diversity in AIDS patients; host immunity can interact with skin microbiota composition as shown in two species of giant salamander; the development of the small intestine microbiome in silka deer; and the gut microbiome of preterm infants that are breastfed develops normally.

Events and jobs

FEMS Project: Volunteer for the Opportunities Board Taskforce

General microbiome

Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists – A. B. F. Ivens – Molecular Ecology

Pregnancy and early life

Maternal antibiotic exposure during pregnancy and hospitalization with infection in offspring: a population-based cohort study – Jessica Eden Miller – International Journal of Epidemiology

*Intestinal microbiota development and gestational age in preterm neonates – Katri Korpela – Scientific Reports

Human oral microbiome

Diversity analysis of subgingival microbial bacteria in peri-implantitis in Uygur population – Gao, Xiaowei MM – Medicine

Human vaginal microbiome

Commentary: The implausible “in vivo” role of hydrogen peroxide as an antimicrobial factor produced by vaginal microbiota – Gilda Tachedjian – Microbiome

Human gut microbiome

Microbiome–host systems interactions: Protective effects of propionate upon the blood–brain barrier – Lesley Hoyles – bioRxiv

*Alterations in the gut microbiota of patients with acquired immune deficiency syndrome – Youlian Zhou – Journal of Cellular and Molecular Medicine

Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons – Amy Wallis – Microbiome

Review: Diet and microbiota linked in health and disease  – T. Requena – Food And Function

Review: The role of gut microbiota and IL-23/IL-17 pathway in ankylosing spondylitis immunopathogenesis: New insights and updates – Farhad Babaie – Immunology Letters

Dissertation: Interaction of Cocoa Powder with Intestinal Microbiota – Zuyin Li – Louisiana State University

Animal experiments

*c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont – Mo Xu – Nature

Dysregulated bile acid synthesis and dysbiosis are implicated in Western diet–induced systemic inflammation, microglial activation, and reduced neuroplasticity – Prasant Kumar Jena – The FASEB Journal

High-fat diet stimulates the gut pathogenic microbiota and maintains hepatic injury in antibiotic-treated rats – Sooad Al-Daihan – Cellular and Molecular Biology

Review: Searching for the gut microbial contributing factors to social behavior in rodent models – Brittany D. Needham – Developmental Neurobiology

Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria – Evelyne Mann – Frontiers in Microbiology

Animal microbiome

*Occupancy strongly influences faecal microbial composition of wild lemurs – Alexander Umanets – FEMS Microbiology Ecology

*Influence of immunogenetics, sex, and body condition on the cutaneous microbial communities of two giant salamanders – Obed Hernández-Gómez – Molecular Ecology

Transient influence of blood meal and natural environment on blacklegged tick bacterial communities – Christine P. Zolnik – Tick and Tick-borne Diseases

The Development of Microbiota and Metabolome in Small Intestine of Sika Deer (Cervus nippon) from Birth to Weaning – Zhipeng Li – Frontiers in Microbiology

Exploring coral microbiome assemblages in the South China Sea – Lin Cai – Scientific Reports

Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea – Esther Rubio-Portillo – Frontiers in Microbiology

Survival and growth of Stenotrophomonas maltophilia in free-living amoebae (FLA) and bacterial virulence properties – Elodie Denet – PLOSone

Gut Microbiota Mediate Insecticide Resistance in the Diamondback Moth, Plutella xylostella (L.) – Xiaofeng Xia – Frontiers in Microbiology

Effects of predation stress and food ration on perch gut microbiota – Yinghua Zha – Microbiome

Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability – Jason A. Rothman – Microbial Ecology

Plant, root, and soil microbiome

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain – Yu Shi – Microbiome

Soil incubation studies with Cry1Ac protein indicate no adverse effect of Bt crops on soil microbial communities – Li Zhaolei – Ecotoxicology and Environmental Safety

The influence of cattle grazing on methane fluxes and engaged microbial communities in alpine forest soils – Mira Mutschlechner – FEMS Microbiology Ecology

Diversity and metabolic potential of the microbiota associated with a soil arthropod – Simon Bahrndorff – Scientific Reports

Soil pH rather than nutrients drive changes in microbial community following long-term fertilization in acidic Ultisols of southern China – Jia Liu – Journal of Soils and Sediments

Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate – Larisa Cortes-Tolalpa – Applied Microbiology and Biotechnology

Commentary: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection

Review: Does genotypic and species diversity of mycorrhizal plants and fungi affect ecosystem function? – Christina Hazard – New Phytologist

Review: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection

Water and extremophile microbiome

Ultra-rare marine microbes contribute to key sulfur related ecosystem functions – Dimitri Kalenitchenko – Molecular Ecology

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Application of metagenome analysis to characterize the molecular diversity and saxitoxin-producing potentials of a cyanobacterial community: a case study in the North Han River, Korea – Keon Hee Kim – Applied Biological Chemistry

Built environment

Airborne microbial communities in the atmospheric environment of urban hospitals in China – Xin-Lei Gao – Journal of Hazardous Materials

Food microbiology

Effects of chitosan oligosaccharides on microbiota composition of silver carp (Hypophthalmichthys molitrix) determined by culture-dependent and independent methods during chilled storage – Shiliang Jia – International Journal of Food Microbiology

Probiotics / prebiotics

Lactobacillus plantarum AN1 cells increase caecal L. reuteri in an ICR mouse model of dextran sodium sulphate-induced inflammatory bowel disease – Yasushi Yokota – International Immunopharmacology

Lactobacillus salivarius LA307 and Lactobacillus rhamnosus LA305 attenuate skin inflammation in mice – S. Holowacz – Beneficial Microbes

Bifidobacteria and its rice fermented products on diet induced obese mice: analysis of physical status, serum profile and gene expressions – M. Ray – Beneficial Microbes

Lactobacillus rhamnosus GG Affects Microbiota and Suppresses Autophagy in the Intestines of Pigs Challenged with Salmonella Infantis – Wei Zhang – Frontiers in Microbiology

Probiotic Use in Equine Gastrointestinal Disease – Angelika Schoster – Veterinary Clinics: Equine Practice

Review: The Role of Prebiotics and Probiotics in Gastrointestinal Disease – Martin H. Floch – Gastroenterology Clinics

Effects of Bentonite Bgp35b-p on the Gut Microbiota of Mice Fed a High-Fat Diet – Eun-Sook Lee – Journal of the Science of Food and Agriculture

Feeding the developing brain: Juvenile rats fed diet rich in prebiotics and bioactive milk fractions exhibit reduced anxiety-related behavior and modified gene expression in emotion circuits – Agnieszka Mika – Neuroscience Letters


Effects of voltage on sulfadiazine degradation and the response of sul genes and microbial communities in biofilm-electrode reactors – Xiao-Li Yang – Ecotoxicology and Environmental Safety

Waste and Pollution

Biodegradation of n-alkanes on oil–seawater interfaces at different temperatures and microbial communities associated with the degradation – Synnøve Lofthus – Biodegradation


The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens – Stefanie U. Wetzels – PLOSone

More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers? – Ylva Lekberg – New Phytologist

Microbes in the news

These Bacteria Digest Toxic Metals And Poop Out Tiny Gold Nuggets – Signe Dean – Science Alert

The discovery of a third form of flagella-mediated motility in symbiotic bacteria – Phys.org

Phage or foe? – In light of new evidence, we have to reassess the role of bacteriophages in microbial communities: are they always the enemy? – Lucía Fernández – npj Biofilms and Microbiomes

The effect of gut bacteria on bone health cannot be generalized – Randi Lundberg – Taconic

Here’s What You Need To Know About The Bacteria In Your Vagina
A microbiome doesn’t just exist in your gut – Sarah DiGiulio – Huffington Post

Understanding Microbial Communities Living On Amphibian Skin – Sofia Prado-Irwin – Science Trends

In the battle against cancer, microbes could be the answer – Nicola Davison – Wired