June 27, 2017

Water microbiome focus today: The effects of terrestrially derived dissolved organic matter on the arctic microbiome, a characterization of deep terrestrial biosphere biofilms, and the microbiome of glaciers and ice sheets.

  • General microbiome

Review: Perspectives and Challenges in Microbial Communities Metabolic Modeling – Emanuele Bosi – Frontiers in Genetics

  • Human respiratory microbiome

Ecological networking of cystic fibrosis lung infections – Robert A Quinn – NPJ Biofilms and Microbiomes

  • Human oral microbiome

Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment – Katy Califf – mSystems

Educational strategies and ART effect on salivary characteristics: a controlled clinical trial – Camila Nobre de Freitas – Oral Diseases

Linkages between oral commensal bacteria and atherosclerotic plaques in coronary artery disease patients – Jyoti Chhibber-Goel – NPJ Biofilms and Microbiomes

Next generation sequencing of oral microbiota in Type 2 diabetes mellitus prior to and after neem stick usage and correlation with serum monocyte chemoattractant-1 – Rubini Anbalagan – Diabetes Research and Clinical Practice

Pyrosequencing Analysis of Cryogenically Ground Samples from Primary and Secondary/Persistent Endodontic Infections – Cangül Keskin – Journal of Endodontics

  • Human gut microbiome

Heat-stabilised rice bran consumption by colorectal cancer survivors modulates stool metabolite profiles and metabolic networks: a randomised controlled trial – Dustin Brown – British Journal of Nutrition

Two rheumatoid arthritis-specific autoantigens correlate microbial immunity with autoimmune responses in joints – Annalisa Pianta – The Journal of Clinical Investigation

Distinct patterns in the gut microbiota after surgical or medical therapy in obese patients – Daniel Medina – PeerJ

Immune-modulating effects in mouse dendritic cells of lactobacilli and bifidobacteria isolated from individuals following omnivorous, vegetarian and vegan diets – Diomira Luongo – Cytokine

  • Animal microbiome

Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands – Ross Cunning – PeerJ

Microbial bioenergetics of coral-algal interactions – Ty Roach – Peer J

Gut symbiont enhances insecticide resistance in a significant pest, the oriental fruit fly Bactrocera dorsalis – Daifeng Cheng – Microbiome

  • Plant, root, and soil microbiome</b

Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils – Meng Wu – Ecotoxicology and Environmental Safety

Disease Suppressive Soils: New Insights from the Soil Microbiome – Daniel Schlatter – Phytopathology

Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides – Wenting Ma – NPJ Biofilms and Microbiomes

  • Water and extremophile microbiome

Review: Constraint-based metabolic modelling of marine microbes and communities – Marco Fondi – Marine Genomics

* Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters – Xiaofen Wu – Microbiome

* The microbiome of glaciers and ice sheets – Alexandre M. Anesio – NPJ Biofilms and Microbiomes

* Microbial Community Response to Terrestrially Derived Dissolved Organic Matter in the Coastal Arctic – Rachel Sipler – Frontiers in Microbiology

  • Built environment

New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures – Wei Cai – Water Research

Architecture, component, and microbiome of biofilm involved in the fouling of membrane bioreactors – Tomohiro Inaba – NPJ Biofilms and Microbiome

  • Techniques

Orthogonal Comparison of GC-MS and 1H NMR Spectroscopy for Short Chain Fatty Acid Quantitation – Jingwei Cai – Anal Chem


June 24, 2017

An early life focus today: Interesting papers on the effects of a pre-term cesarian birth on the gut microbiome and the impact of the infant gut microbiome on food allergies. Also highlighted, the relationship between the gut microbiome and social stress vulnerability in mice, the role of the gut microbiome in mosquito development, and evidence of a permanent transfer of prokaryotic virus sequences to the mammalian brain.

  • Pregnancy and early life

Review: Perinatal Group B Streptococcal Infections: Virulence Factors, Immunity, and Prevention Strategies – Jay Vornhagen – Trends in Microbiology

* Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants – Christopher Stewart – Frontiers in Microbiology

* A prospective microbiome-wide association study of food sensitization and food allergy in early childhood – Jessica Savage – Allergy

  • Human respiratory microbiome

Psl Produced by Mucoid Pseudomonas aeruginosa Contributes to the Establishment of Biofilms and Immune Evasion – Christopher Jones – mBio

  • Human skin microbiome

Isotretinoin and lymecycline treatments modify the skin microbiota in acne – Hanna-Lenna Kelhala – Experimental Dermatology

  • Human oral microbiome

Potassium is a key signal in host-microbiome dysbiosis in periodontitis – Susan Yost – PLOS Pathogens

  • Human gut microbiome

The TMAO-Producing Enzyme Flavin-Containing Monooxygenase 3 Regulates Obesity and the Beiging of White Adipose Tissue – Rebecca Schugar – Cell Reports
In vitro modulation of gut microbiota by whey protein to preserve intestinal health – Sanchez-Moya – Food and Function

Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis – Gregory Young – Frontiers in Cellular and Infection Microbiology

NOD2 genetic variants predispose one of two familial adenomatous polyposis siblings to pouchitis through microbiome dysbiosis – Kathleen Schieffer – Journal of Crohn’s and Colitis

The Bacteroides fragilis pathogenicity island links virulence and strain competition – Benjamin Casterline – Gut Microbes

Diversity analysis of gut microbiota in osteoporosis and osteopenia patients – Jihan Wang – PeerJ

Gut microbiota of liver transplantation recipients – Li-Ying Sun – Scientific Reports

Review: Microbiome: A Potential Component in the Origin of Mental Disorders – George Stefano – Medical Science Monitor

Review: Impact of mycotoxins on the intestine: are mucus and microbiota new targets? – Herve Robert – Journal of Toxicology and Environmental Health

Review: Microbiota, Inflammation and Colorectal Cancer – Cecily Lucas – International Journal of Molecular Sciences

Review: The Enteric Network: Interactions between the Immune and Nervous Systems of the Gut – Bryan Yoo – Immunity

  • Cadaver microbiome

Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition – Javier Pascual – Environmental Microbiology


  • Animal experiments

* Implications of the gut microbiota in vulnerability to the social avoidance effects of chronic social defeat in male mice – Joanna Kasia Szyszkowicz – Brain, Behavior, and Immunity

Intestinal microbial dysbiosis aggravates the progression of Alzheimer’s disease in Drosophila – Shih-Cheng Wu – Nature Communications

Fructo-oligosaccharides and intestinal barrier function in a methionine-choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS One

Spirulina Protects against Hepatic Inflammation in Aging: An Effect Related to the Modulation of the Gut Microbiota? – Audrey Neyrinck – Nutrients

Antrodia cinnamomea reduces obesity and modulates the gut microbiota in high-fat diet-fed mice – C.J Chang – International Journal of Obesity

Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by Staphylococcus aureus competitors – Adam SanMiguel – Antimicrobial Agents and Chemotherapy

Temporal microbiota changes of high-protein diet intake in a rat model – Chunlong Mu – Anaerobe

  • Animal microbiome

Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO2 – Guowei Zhou – Environmental Microbiology

Effects of dietary supplementation of red pepper (Schinus terebinthifolius Raddi) essential oil on performance, small intestinal morphology and microbial counts of weanling pigs – Pedro Leon Gomes Cairo – Science of Food and Agriculture

Identification of Bufadienolides from the Boreal Toad, Anaxyrus boreas, Active Against a Fungal Pathogen – Kelly Barnhart – Microbial Ecology

* Bacteria-mediated hypoxia functions as a signal for mosquito development – Kerri Coon – PNAS

  • Plant, root, and soil microbiome

The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation – Eduardo de Siva Fonseca – Microbial Ecology

  • Water and extremophile microbiome

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses – Vera Thiel – Frontiers in Microbiology


  • Phages and viruses

* A prokaryotic viral sequence is expressed and conserved in mammalian brain – Yang-Hui Yeh – PNAS

  • Techniques

Solid Sampling with a Diode Laser for Portable Ambient Mass Spectrometry – Yeni Yung – Analytical Chemistry

June 16, 2017

Gut microbiome focus: Differences in the gut microbiome between children and adults can mediate the metabolism of arsenic possibly leading to differences in exposure risk, the gut microbiome’s ability to protect against salmonella infection is dependent on the IFNy producing bacteria, the microbiome of insoluble fibre is characterized, and a new in vitro technique to interrogate intestinal transport of microbiota and antigens. Plus an overview of the world data centre for microorganisms, and MicroScope for microbial genome annotation. 

  • Events and jobs

Microbiology Technologist OR Microbiology Medical Technologist – Orlando Florida  


  • General microbiome

Conference: Current concepts in chronic inflammatory diseases: Interactions between microbes, cellular metabolism, and inflammation – Holger Garn – Allergy and Clinical Immunology

  • Human oral microbiome

Characterisation of Roseomonas mucosa isolated from the root canal of an infected tooth – Nina Diesendorf – BMC Research Notes

  • Human gut microbiome

* Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model – Naiyi Yin – Chemosphere

* Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome – Kim De Paepe – Environmental Microbiology

Review: Microbiota Therapy for Clostridium difficile and Antibiotic Resistant Enteric Infections – Brittany Lewis – Annual Review of Microbiology


  • Animal experiments

* Enhancement of IFNγ Production by Distinct Commensals Ameliorates Salmonella-Induced Disease – Sophie Thiemann – Cell Host and Microbe

Efficacy of antibiotic treatment of implant-associated Staphylococcus aureus infections with moxifloxacin, flucloxacillin, rifampin, and combination therapy: an animal study – Felix Greimel – Drug Design, Development and Therapy

The scales of the zebrafish: host–microbiota interactions from proteins to populations – Adam Burns – Current Opinion in Microbiology

IL-17 Receptor A Maintains and Protects the Skin Barrier To Prevent Allergic Skin Inflammation – Achilleas Floudas – The Journal of Immunology

Irf4-dependent CD103+CD11b+ dendritic cells and the intestinal microbiome regulate monocyte and macrophage activation and intestinal peristalsis in postoperative ileus – Judith-Mira Pohl – Gut

  • Animal microbiome

Effect of three lactobacilli with strain-specific activities on the growth performance, faecal microbiota and ileum mucosa proteomics of piglets – Yating Su – Journal of Animal Science and Biotechnology

  • Plant, root, and soil microbiome

Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis – Cameron Habib – PLOSone

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function – Sebastian Flues – Environmental Microbiology

Green alder (Alnus viridis) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently – G Schwob – Environmental Microbiology

The role of organic acids on microbial deterioration in the Radix pseudostellariae rhizosphere under continuous monoculture regimes – Hongmiao Wu – Scientific Reports

Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization – María Eugenia Salas – Environmental Microbiology

  • Water and extremophile microbiome

Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean – SJ Goldberg – Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment, and water bacterial communities – Arthur Escalas – Environmental Microbiology


  • Phages and viruses

Preprint: Bacteria defend against phages through type IV pilus glycosylation – Hanjeong Harvey- bioRxiv

  • Techniques

Dissecting the human microbiome with single-cell genomics – Andrew Tolonen – Genome Medicine

* A human intestinal M-cell-like model for investigating particle, antigen and microorganism translocation – Ana Beloqui – Nature Protocols

  • Metagenomics

* World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide – Linhuan Wu – Nucleic Acids Research

* MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes – David Vallenet – Nucleic Acids Research

Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome – Fergus Collins – Scientific Reports

Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil – Leli Tang – Gene

  • Microbial Physiology

Preprint: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli – Paramita Sarkar – bioRxiv

Preprint: Campylobacter jejuni transcriptome changes during loss of culturability in water – Christina Bronowski – bioRxiv


  • Microbes in the news

You Are What You Eat, And What You Eat Is Millions of MicrobesKyle Frischkorn – Smithsonian.com

John Bartlett’s Take on Critical Infectious Disease Topics: Part 3 – John Bartlett – Medscape

Placental Microbiome – Sally Robertson – Life Sciences News

Light-activated bacteria protect rats from heart attacks – Michael Price – Science

These light-eating bacteria could one day help us survive heart attacks – Alessandra Potenza – The Verge

Scientists image molecular machinery never before seen in bacteria – Brooke Hays – UPI

February 25, 2017

Insight into the role of gut microbiome lipid metabolites in central nervous system diseases. A role of invasive plants in altering the soil microbiome. Evidence that microbiome alterations in Crohn’s disease are not genetically based.

Events and jobs

Post-Doctoral Research Associate in immunology, microbiology, virology, and/or biochemistry – MRIGlobal, Gaithersburg, Maryland, USA

Research Scientist – Department of Microbiology – University of Illinois at Urbana-Champaign, USA

Part-Time Microbiology Instructor – Foothill-De Anza Community College District, California, USA

First Stage Researcher with background in environmental microbiology – Faculty of Biology, University of Warsaw, Poland

General microbiome

Altered antibiotic tolerance in anaerobic digesters acclimated to triclosan or triclocarban – Daniel E. Carey – Chemosphere

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases and Other Escherichia coli Isolated from Food of Animal Origin and Human Intestinal Isolates – Krizman M – Journal of Food Protection

Human oral microbiome

Prospective, randomised, controlled study evaluating early modification of oral microbiota following admission to the intensive care unit and oral hygiene with chlorhexidine – Felipe Francisco Tuon – Journal of Global Antimicrobial Resistance

The potential effect of oral microbiota in the prediction of mucositis during radiotherapy for nasopharyngeal carcinoma -Xiao-Xia Zhu – EBioMedicine

Human urinary microbiome

*Special Issue Preface: Preface to the human microbiome in urologic health and disease – Daniel A. Shoskes – Annals of Translational Medicine

*Review: The mycobiome of the human urinary tract: potential roles for fungi in urology – A. Lenore Ackerman – Annals of Translational Medicine

Human vaginal microbiome

Longitudinal analysis of vaginal microbiota in women with recurrent vulvovaginal candidiasis – Ma X – Journal of Southern Medical University (Nan Fang Yi Ke Da Xue Xue Bao)

Human gut microbiome

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLOS

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z.D Jiang – Alimentary Pharmacology and Therapeutics

Gut-brain axis: Role of lipids in the regulation of inflammation, pain and CNS diseases – Russo R – Current Medicinal Chemistry

What roles do colon stem cells and gap junctions play in the left and right location of origin of colorectal cancers? – James E. Trosko – Journal of Cell Communication and Signaling

Contributions of the Interaction between Dietary Protein and Gut Microbiota to Intestinal Health – Ma N – Current Protein and Peptide Science

*Review: Dietary Fiber Gap and Host Gut Microbiota – Han M – Protein Peptide Letters

Structural Modulation of Gut Microbiota during Alleviation of Antibiotic-Associated Diarrhea with Herbal Formula – Weijie Lv – International Journal of Biological Macromolecules

Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods – E. Tajeddin – European Journal of Clinical Microbiology & Infectious Disease

Immunomodulatory Effects of Lactobacillus plantarumLp62 on Intestinal Epithelial and Mononuclear Cells – Thalis Ferreira dos Santos – BioMed Research International

How to modulate gut microbiota: diet, pre-probiotics or antibiotics? – Ponziani FR – Minerva Gastroenterologica E Dietologica

* Review: AISF position paper on nonalcoholic fatty liver disease (NAFLD): Updates and future directions – Italian Association for the Study of the Liver (AISF), Lonardo A – Digestive and Liver Disease

Clostridium difficile infection in acute flares of inflammatory bowel disease: A prospective study -Harry Sokol – Digestive and Liver Disease

 Multi-site human microbiome

Porphyromonas gingivalis lipopolysaccharide induces pro-inflammatory adipokine secretion and oxidative stress by regulating Toll-like receptor-mediated signaling pathways and redox enzymes in adipocytes – Fanny Le Sage – Molecular and Cellular Endocrinology

Animal experiments

Impact of TIGECYCLINE versus other antibiotics on the fecal metabolome and on colonization resistance to CLOSTRIDIUM DIFFICILE in mice – Robin L.P. Jump – Pathological Immunology

Animal microbiome

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird – Jakub Kreisinger – Frontiers in Microbology

Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts – Gitta Szabó – The ISME Journal

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11 – Lindsey M Solden – The ISME Journal

Changes in rumen microbiota composition and in situ degradation kinetics during the dry period and early lactation as affected by rate of increase of concentrate allowance – K. Dieho – Journal of Dairy Science

Plant, root, and soil microbiome

Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra – Lin Li – Scientific Reports

Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants – Sevda Haghi Kia – The ISME Journal

Comparative fibre-degrading capacity in foals at immediate and late post-weaning periods – C. Faubladier – Cambridge Core

The effect of the source of microorganisms on adaptation of hydrolytic consortia dedicated to anaerobic digestion of maize silage – Krzysztof Poszytek – Anaerobe

Water and extremophile microbiome

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle – Nathan Cermak – The ISME Journal

Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts – Rachel Ashley Levin – The ISME Journal

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton – Ryan W Paerl – The ISME Journal

Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment – Nestor Arandia-Gorostidi – The ISME Journal

Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms – Lijuan Ren – The ISME Journal

Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities – Ryan de Montmollin Jennings – Frontiers in Microbiology

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes – Md Sainur Samad – Frontiers in Microbiology

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor – Jiasong Fang – Frontiers in Microbiology

Metagenomics and resistome

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection – Li-Guan Li – The ISME


Assessment of the bimodality in the distribution of bacterial genome sizes – Hyun S Gweon – The ISME Journal

Genome of ‘Ca. Desulfovibrio trichonymphae’, an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut – Hirokazu Kuwahara – The ISME Journal

A family of interaction-adjusted indices of community similarity – Thomas Sebastian Benedikt Schmidt – The ISME Journal

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates – Po-Hsiang Wang – The ISME Journal

Phylogenetic relationships among Staphylococcus aureus isolated from clinical samples in Mashhad, Iran – Farzad Khadem – Journal of Infection and Public Health

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex – Abraham Morales-Cruz – Molecular Plant Pathology

More microbes

Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens – Caleb E Levar – The ISME Journal

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability – Erin F E Lennon – The ISME Journal

Enhanced microbial electrosynthesis by using defined co-cultures – Jörg S Deutzmann – The ISME Journal

Temperature is a key factor in Micromonas–virus interactions – David Demory – The ISME Journal

Evolutionary convergence in experimental Pseudomonas populations – Peter A Lind – The ISME Journal

Microbes in the news

Are There Health Benefits To Exposing Our Immune Systems To Bacteria? – Forbes
Nutrition: Trust your gut instincts — whole grains are good for you – Los Angeles Daily News

There could be a surprising link between how people respond to a new cancer treatment and their microbiome – Lydia Ramsey – Business Insider

February 11, 2017

Changes in the gut microbiota during aging is associated with increased gut permeability and peripheral inflammation and may mediate cognitive decline. An overview of the gut microbiome in Crohn’s Disease and insight into how extremophiles might maintain protein folding. 

General microbiome

Whole genome sequence of lactic acid bacterium Pediococcus acidilactici strain S1 – Gun-Seok Park  Brazilian Journal of Microbiology

Pygmaiobacter massiliensis’ sp. nov., a new bacterium isolated from the human gut of a Pygmy woman – M. Bilen – NMNI

Human and rat gut microbiome composition is maintained following sleep restriction – Zhang SL – PNAS

Palaeogeographic variation in the Permian−Triassic boundary microbialites: A discussion of microbial and ocean processes after the end-Permian mass extinction – Stephen Kershaw – Journal of Palaeogeography

Assessment of bacterial profiles in aged, home-made Sichuan paocai brine with varying titratable acidity by PacBio SMRT sequencing technology – Jialu Cao – Food Control


Human gut microbiome

A microbial signature for Crohn’s disease – Victoria Pascal – Gut

Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets  – V. Shankar – mSystems

*PrePrint:  Postmortem succession of gut microbial communities in human cadavers – Jennifer M DeBruyn – PeerJ Preprints

Substituting whole grains for refined grains in a 6-wk randomized trial has a modest effect on gut microbiota and immune and inflammatory markers of healthy adults – Vanegas SM – American Journal of Clinical Nutrition

Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis – Hai-Ning Liu – Digestive and Liver Disease

Animal experiments 

Revisiting Metchnikoff: Age-related Alterations in Microbiota-Gut-Brain Axis in the Mouse – Karen A. Scott – Brain, Behavior, and Immunity

Animal microbiome 

Immune system stimulation by the native gut microbiota of honey bees – Waldan K. Kwong – Royal Society for Open Science

Deep Sequencing Reveals Highly Variable Gut Microbial Composition of Invasive Fish Mossambicus Tilapia (Oreochromis mossambicus) Collected from Two Different Habitats – Swapnil Sopan Gaikwad – Indian Journal of Microbiology

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica –  Ngare Wilkinson – Environmental Biotechnology

Plant, root, and soil microbiome

Hydrogen Peroxide and Strigolactones Signaling Are Involved in Alleviation of Salt Stress Induced by Arbuscular Mycorrhizal Fungus in Sesbania cannabina Seedlings – Cun-Cui Kong – Journal of Plant Growth Regulation

Potential Role of Plant-Associated Bacteria in Plant Metal Uptake and Implications in Phytotechnologies – Petra S. Kidd – Advances in Botanical Research

Application of bacteria from non-cultivated plants to promote growth, alter root architecture and alleviate salt stress of cotton – Ivelisse Irizarry – Journal of Applied Microbiology

*Reference:  Phytomyxea – Simon Bulman – Springer Reference – Handbook of the Protists

Water and extremophile microbiome 

Molecular determinant of the effects of hydrostatic pressure on protein folding stability – Calvin R. Chen – Nature Communications

Microarray analysis of the benthic bacterium Shewanella piezotolerans WP3 at low temperature – Huahua Jian – Marine Genomics

Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India – Abhishek Gupta – Genomics Data

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes – Yu Wan – Microbiology Open

Variations in airborne bacterial communities at high altitudes over the Noto Peninsula (Japan) in response to Asian dust events – Teruya Maki – Atmospheric Chemistry and Physics Discussions

Phages and viruses

Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples – Thannesberger J – The FASEB Journal


Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Llado – PLOS one

Cultivation-Free Raman Spectroscopic Investigations of Bacteria – Björn Lorenz – Trends in Microbiology

*Review:  Proteomics Tracing the Footsteps of Infectious Disease – Todd M Greco – Molecular and Cellular Proteomics

Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine – Michel Fredérich – Journal of Medical Chemistry

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data – Wadsworth WD – BMC Bioinformatics

Microbes on the market 

Lipid accumulation in prokaryotic microorganisms from arid habitat – Philippa Hauschild – Applied Microbiology and Biotechnology



January 19, 2017

Pollen has a microbiome. The mode of birth and breastfed status correlates with alterations in the gut microbiome and urine metabolome of children. A catalog of the gut microbiome of the Tyrolean Iceman and ancient bacteria strains. And, the first evidence that phages coordinate their lysis–lysogeny (active-dormant) phases with each other, and even inter-generationally, via small molecule signalling.

  • Events and jobs

Lab Technician – Microbiology – GMP – Cambridge – £16k – New Scientist

Podcast: Gut Bacteria and Parkinson’s Connection – Maggie McGuire Kuhl – The Michael J Fox Foundation for Parkinson’s Research

  • General microbiome

Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age – Gabriele Andrea Lugli – Microbiome

  • Pregnancy and early life

Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort – Cian J. Hill – Microbiome

Oral colostrum priming shortens hospitalization without changing the immunomicrobial milieu – J Romano-Keeler – Journal of Perinatology

  • Multi-site human microbiome

Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease – Johanna Klughammer – PLOSone

  • Human respiratory microbiome

The effect of cigarette smoking on the oral and nasal microbiota – Guoqin Yu – Microbiome

Bacterial community collapse: a meta-analysis of the sinonasal microbiota in chronic rhinosinusitis – Brett Wagner Mackenzie – Environmental Microbiology

  • Human skin microbiome

Review – Cyanobacterial metabolites as a source of sunscreens and moisturizers: a comparison with current synthetic compounds – Peyman Derikvand – European Journal of Phycology

  • Human gut microbiome

Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals – M. Andrea Azcarate-Peril – PNAS

  • Animal experiments

Drosophila Genotype Influences Commensal Bacterial Levels – Angela M. Early – PLOSone

Lactobacillus rhamnosus GR-1 Attenuates Induction of Hypertrophy in Cardiomyocytes but not through Secreted Protein MSP-1 (p75) – Grace Ettinger – PLOSone

  • Animal microbiome

Happens in the best of subfamilies: establishment and repeated replacements of co-obligate secondary endosymbionts within Lachninae aphids – Alejandro Manzano-Marín – Environmental Microbiology

Evolution of new sex chromosomes by lateral genome transfer of bacterial symbiont in pillbug – Richard Cordaux – Journal 2016 International Congress of Entomology

  • Plant, root, and soil microbiome

Pollen has a microbiome: implications for plant reproduction, insect pollination and human allergies – Michael Zasloff – Evironmental Microbiology

Phosphorus acquisition efficiency in arbuscular mycorrhizal maize is correlated with the abundance of root-external hyphae and the accumulation of transcripts encoding PHT1 phosphate transporters – Ruairidh J. H. Sawers – New Phytologist

  • Water and extremophile microbiome 

Coastal bacterioplankton community response to diatom-derived polysaccharide microgels – Joe D Taylor – Environmental Microbiology Reports

Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean – Wenxue Wu – Environmental Microbiology

  • Built environment

Effect of temperature and colonization of Legionella pneumophila and Vermamoeba vermiformis on bacterial community composition of copper drinking water biofilms – Helen Y. Buse – Microbial Biotechnology

  • Phages and viruses

Communication between viruses guides lysis–lysogeny decisions – Zohar Erez – Nature

  • Bioinformatics and Databases

Data from: Network structure and local adaptation in coevolving bacteria-phage interactions – Gurney J, Aldakak – Dryad Digital Repository

  • Techniques

Optical sorting and cultivation of denitrifying anaerobic methane oxidation archaea – Xiaoqiong Qi – Biomedical Optics Express

  • Microbes in the news 

Friends for life: human microbiota – E.M. Bik – uBiome

Advancing Phage Therapy  -Joanna Urban – American Society for Microbiology

Bacteria-Treated Mosquitoes Released in More Locations – Kerry Grens – The Scientist

Asgard Archaea Hint at Eukaryotic Origins – Joshua A. Krisch – The Scientist

UNC researchers lead study of prebiotic recomposition in gut microbiome for lactose intolerance – Life Science Daily News Desk

Breastmilk crucial to aid premature C-section babies – Joyce Fegan – Irish Examiner

New study provides insight into fighting drug-resistant bacteria – Isabelle Doan – The Chronicle

Snow microbes used in art – Matt Brooks – WTHITV10

  • Microbes on the market 

Rebiotix, Mayo Team Up To Test Orally-Administered Gut Microbe Transplant – Don Jacobson – Twin Cities Business