March 27, 2017

Exploring life within the biofilm and how free-living microbes thrive, and focus on life history patterns of symbionts. Finally, big dairy (Parmalat- South Africa)  was found guilty of repeatedly hiding serious infections (Salmonella and Listeria,)from their consumers.

General microbiome

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions.

Wang D. ISME Journal

Symbiont Acquisition and Replacement as a Source of Ecological Innovation.

Sudakaran S. Trends in Microbiology

Distinct succession patterns of abundant and rare bacteria in temporal microcosms with pollutants.

Jiao S. Environmental Pollution

Similar articles

Human gut microbiome

Early-life origin of intestinal inflammatory disorders.

Ley D. Nutrition Reviews

From mystery to mechanism: Can proteomics build systems-level understanding of our gut microbes?

Gonzalez CG. Expert Reviews of Proteomics

Human oral microbiome

Circadian oscillations of microbial and functional composition in the human salivary microbiome.

Takayasu L. DNA Research

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.

Yamagishi J.PLoS One.

Water, estuarine and marine microbiome

Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics.

Moitinho-Silva L. ISME Journal

Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes.

Berry MA. Frontiers in Microbiology

Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens.

Mohiuddin MM. Water Research

Symbiosis and microbiome flexibility in calcifying benthic foraminifera of the Great Barrier Reef.

Prazeres M. Microbiome

Farm animal microbiome

Effects of dietary rapeseed meal supplementation on cecal microbiota in laying hens with different flavin-containing monooxygenase 3 genotypes.

Long C. Poultry Science

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot.

Maboni G. Scientific Reports

Pasture flock chicken cecal microbiome responses to prebiotics and plum fiber feed amendments.

Park SH. Poultry Science

Respiratory system microbiome

Dendritic cell expression of the signaling molecule TRAF6 is required for immune tolerance in the lung.

Han D. International Immunology

Eukaryote microbiome

UniEuk: Time to Speak a Common Language in Protistology!

Berney C. The Journal of Eukaryotic Microbiology

Animal microbiome

Colonization by non-pathogenic bacteria alters mRNA expression of cytochromes P450 in originally germ-free mice.

Jourová L. Folia Microbiologica

Gut microbiome-related metabolic changes in plasma of antibiotic-treated rats.

Behr C. Archives of Toxicology

Indoor microbiome

Hospital microbial surface colonization revealed during monitoring of Klebsiella spp., Pseudomonas aeruginosa, and non-tuberculous mycobacteria.

Geadas Farias P. Antonie Van Leeuwenhoek

Microbes in the news

Parmalat hides bacteria infections

-News24

Indians find a new bacterial target for drug development

-The Hindu

March 22, 2017

Today’s digest features interesting review articles on the role of microbiome in health and disease, heart failure, and how the respiratory tract microbiota act as gatekeepers to respiratory health. Also, we have original research articles on the response of bacterial communities in oil-contaminated marine waters to addition of chemical and biological dispersants. Also, a very fascinating article in Harvard Business review on the gender bias against junior female scientists. Not surprising!! Enjoy.

General microbiome

*Review: The role of the microbiome in human health and disease: an introduction for clinicians – Vincent B Young – British Medical Journal

*Review: Targeting the Microbiome in Heart Failure – Allyson Zabell – Current Treatment Options in Cardiovascular Medicine

Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China – Guoqin Yu – international Journal of Cancer

Pregnancy and early life

Late preterm birth has direct and indirect effects on infant gut microbiota development during the first six months of life – M Forsgren – Acta Pediatrica

Vaginal microbiome

Characterization of vaginal Lactobacillus species by rplK -based multiplex qPCR in Russian women – Vladimir V. Demkin – Anaerobe

Human oral microbiome

Changes in salivary microbiota increase volatile sulfur compounds production in healthy male subjects with academic-related chronic stress – Bruno Dias Nani – Plos One

Candida albicans biofilm heterogeneity does not influence denture stomatitis but strongly influences denture cleansing capacity – Lindsay E. O’Donnell – Journal of Medical Microbiology

Oral Bacterial Infections : Diagnosis and Management – Glendee Reynolds-Campbell – Dental Clinics of North America

Human respiratory microbiome

*The microbiota of the respiratory tract: gatekeeper to respiratory health – Wing Ho Man – Nature Reviews Microbiology

Human gut microbiome

Editorial : Infant colic is still a mysterious disorder of the microbiota–gut–brain axis – Anna Pärtty – Acta Pediatrica

Review: More Flavor for Flavonoid-Based Interventions? – Nadeem O. Kaakoush – Trends in Molecular Medicine

Perspectives : New Frontiers in Fibers: Innovative and Emerging Research on the Gut Microbiome and Bone Health – Taylor C. Wallace – Journal of the American College of Nutrition

Does the Gut Microbiota Influence Immunity and Inflammation in Multiple Sclerosis Pathophysiology? – Monika Adamczyk-Sowa – Journal of Immunology Research

The Role of Intestinal Alkaline Phosphatase in Inflammatory Disorders of Gastrointestinal Tract – Jan Bilski – Mediators of Inflammation

The Gut Microbiome, Energy Homeostasis, and Implications for Hypertension – Ruth A. Riedl – Current Hypertension Reports

Fecal Microbiota Transplantation

Commentary: A proposed definition of microbiota transplantation for regulatory purposes – Diane E. Hoffmann – Gut Microbes

Review: Novel Indications for Fecal Microbial Transplantation: Update and Review of the Literature – Nathaniel Aviv Cohen – Digestive Diseases and Sciences

Animal microbiome

Review: Role of the microbiome in swine respiratory disease – Megan C. Niederwerder – Veterinary Microbiology

Comparative composition, diversity, and abundance of oligosaccharides in early lactation milk from commercial dairy and beef cows – William M. Sischo – Journal of Dairy Science

Comparative analysis of fecal microbial communities in cattle and Bactrian camels – Liang Ming – Plos One

Sheep fed with banana leaf hay reduce ruminal protozoa population – Cláudio Eduardo Silva Freitas – Tropical Animal Health and Production

Metabolomics

Review: Metabolomic-guided discovery of Alzheimer’s disease biomarkers from body fluid – Che Nor Adlia Enche Ady – Journal of Neuroscience Research

Animal experiments

The farming environment protects mice from allergen-induced skin contact hypersensitivity – C. P. Frossard – Clinical and Experimental Allergy

Metabolomics insights into diabetes nephropathy and protective effects of Radix Scutellariae on rats using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry – Lihui Men – RSC Advances

Plant, root, and soil microbiome

Root plant growth promoting rhizobacteria inoculations increase ferric chelate reductase (FC-R) activity and Fe nutrition in pear under calcareous soil conditions – Muzaffer İpek – Scientia Horticulturae

Bacterial diversity of the rhizosphere and nearby surface soil of rice (Oryza sativa) growing in the Camargue (France) – Jorge R. Osman – Rhizosphere

Structure and function of the bacterial communities during rhizoremediation of hexachlorobenzene in constructed wetlands – Cuiping Zhang – Environmental Science and Pollution Research

Water and extremophile microbiome
Characterization of spatial distribution of the bacterial community in the South Sea of Korea – Ji-Hui Seo – Plos One

Diversity and community structure of cyanobacteria and other microbes in recycling irrigation reservoirs – Ping Kong – Plos One

*Response of the bacterial community in oil-contaminated marine water to the addition of chemical and biological dispersants – Camila Rattes de Almeida Couto – Journal of Environmental Management

Probiotics / prebiotics

Lactobacillus johnsonii supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation – W. Fonseca- Mucosal Immunology

Identification of the key excreted molecule by Lactobacillus fermentum related to host iron absorption – Ana González – Food Chemistry

Effect of 8-weeks prebiotics/probiotics supplementation on alcohol metabolism and blood biomarkers of healthy adults: a pilot study – Christopher Irwin – European Journal of Nutrition

Bioinformatics

Making big data smart—how to use metagenomics to understand soil quality – Gisle Vestergaard – Biology and Fertility of Soils

Techniques

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? – Monika Balvočiūtė – BMC Genomics

Comparative evaluation of four bacteria-specific primer pairs for 16S rRNA gene surveys – Sofie Thijs – Frontiers in Microbiology

Microbes in the news

Asthma: Researchers discover how exposure to microbes protects against asthma

Rainy Day? Microbes May Be at Play

Building A Brewery, Chapter 4: For the Love of Microbes

Science, publishing, and career 

*Junior Female Scientists Aren’t Getting the Credit They Deserve “despite evidence that women on average, may perform better than men in early stage of their careers”

Anitha’s non-microbiology picks

How Pluto’s haze could explain its red spots

Cancer cells cast a sweet spell on the immune system

Actinide chemistry expands to new oxidation states

March 15, 2017

Today’s digest is full of environmental, soil/plant/root, and water related studies among a few gut microbiome studies and some opinion pieces.

Events and jobs

Event: Gut Feeling – How bacteria influence our wellbeing – EMBL-EBI – 21-May-2017

Event: Meeting of the Microbiome Minds – Colorado State University

General microbiome

Opinion: The study of microbiota needs both microbiologists and medical doctors – Didier Raoult – CMI

Pregnancy and early life

Review: Distinct Roles of Cervical Epithelia and Stroma in Pregnancy and Parturition – Shanmugasundaram Nallasamy – Seminars in Reproductive Medicine (Thieme)

The shape of the microbiome in early life – Erika von Mutius – Nature Medicine

Multi-site human microbiome

Examination of Host Phenotypes in Gambusia affinis Following Antibiotic Treatment – Jeanette M. Carlson – J. Vis. Exp.

Human respiratory microbiome

Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa – Laurence Pages-Monteiro – PLOS One

Human skin microbiome

Review: Cutaneous wound biofilm and the potential for electrical stimulation in management of the microbiome – Mohammed Ashrafi – Future Microbiology

Human vaginal microbiome

Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, an Sexually Transmitted Diseases – Felicia M. Lewis – Obstetrics & Gynecology

Women view key sexual behaviours as the trigger for the onset and recurrence of bacterial vaginosis – Jade E. Bilardi – PLOS One

Human oral microbiome

Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study – Sebastien Boutin – Frontiers in Microbiology

Human gut microbiome

*The altered gut microbiota in adults with cystic fibrosis – D.G. Burke – BMC Microbiology

Consumption of a diet rich in Brassica vegetables is associated with a reduced abundance of sulphate-reducing bacteria: a randomised crossover study – Lee Kellingray – Molecular Nutrition & Food Research

Gastric Acid Suppression Is Associated with an Increased Risk of Adverse Outcomes in Inflammatory Bowel Disease – Shah R – Digestion

NLRP12 attenuates colon inflammation by maintaining colonic microbial diversity and promoting protective commensal bacterial growth – Liang Chen – Nature Immunology

Gut microbiome diversity and high fibre intake are related to lower long term weight gain – Menni C – International Journal of Obesity

We are not alone: a case for the human microbiome in extra intestinal diseases – S. Shivaji – Gut Pathogens

The intestinal microenvironment in sepsis – Katherine T Fay – BBA – Molecular Basis of Disease

The Gut Microbiome and Its Role in Cardiovascular Diseases – W. H. Wilson Tang – Circulation

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Mechanisms and effects of arsanilic acid on antibiotic resistance genes and microbial communities during pig manure digestion – Wei Sun – Bioresource Technology

Dietary Broccoli Alters Rat Cecal Microbiota to Improve Glucoraphanin Hydrolysis to Bioactive Isothiocyanates – Xiaoji Liu – Nutrients

Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens – Eduardo Crisol-Martinez – PeerJ

Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E−/− mice – Paul M. Ryan – Microbiome

Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome – Daniel Aguirre de Cárcer – PLOS One

Animal microbiome (for animals in the wild)

Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time – Sheila Torres – PeerJ

Fine Flounder (Paralichthys adspersus) Microbiome Showed Important Differences between Wild and Reared Specimens – Carolina Ramirez – Frontiers in Microbiology

Use of signature-tagged mutagenesis to identify genes associated with colonization of sheep by E. coli O157:H7 – Nancy A. Cornick – Veterinary Microbiology

The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential – Ciro Cesar Rossi – Veterinary Microbiology

The bovine paranasal sinuses: Bacterial flora, epithelial expression of nitric oxide and potential role in the in-herd persistence of respiratory disease pathogens – Gerard M. Murray – PLOS One

Plant, root, and soil microbiome

Analysis of microbiota involved in the aged natural fermentation of indigo – Takahiro Okamoto – World Journal of Microbiology and Biotechnology

Microbial solvent formation revisited by comparative genome analysis – Anja Poehlein – Biotechnology for Biofuels

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities – Wepking, C – Proceedings of the Royal Society B-Biological Science

Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms – Tobias Weil – Microbiome

Characterization of microbial communities during start-up of integrated fixed-film activated sludge (IFAS) systems for the treatment of oil sands process-affected water (OSPW) – Chunkai Huang – Biochemical Engineering Journal

Effects of experimental addition of nitrogen and phosphorus on microbial and metazoan communities in a peatbog – Tomasz Mieczan – European Journal of Protistology

The potential of native species as bioenergy crops on trace-element contaminated Mediterranean lands – Dominquez MT – Sci Total Environment

Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar – Jaiswal AK – Scientific Reports

Growth and 137Cs uptake and accumulation among 56 Japanese cultivars of Brassica rapa, Brassica juncea and Brassica napus grown in a contaminated field in Fukushima: Effect of inoculation with a Bacillus pumilus strain – Salem Djedidi – Journal of Environmental Radioactivity

Antibiotic mixture effects on growth of the leaf-shredding stream detritivore Gammarus fossarum – Mirco Bundschuh – Ecotoxicology

Microbial community changes during different empty bed residence times and operational fluctuations in an air diffusion reactor for odor abatement – Elisa Rodriguez – Science of the Total Environment

Response of indigenously developed bacterial consortia in progressive degradation of polyvinyl chloride – Mohammad S Anwar – Protoplasma

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

Conference: Effects of simulated deep-sea mining impacts on microbial communities and functions in the DISCOL experimental area – Vonnahme, T – EU FP7 MIDAS final meeting,

Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities – Wei Xing – Journal of Environmental Sciences

PrePrint: Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive2 presence of metal resistance genes – Ankita Kothari – bioRxiv

Climate, soil and plant functional types as drivers of global fine-root trait variation – Gregoire T. Freschet – Journal of Ecology

Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function – Konstantin Gavazov – Science of the Total Environment

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes – Emily B. Graham – Environmental Microbiology

Review: Microbiome involved in microbial electrochemical systems (MESs): A review – Saratale RG – Chemosphere

Chapter Four – Polar Marine Microorganisms and Climate Change – C. Verde – Advances in Microbial Physiology

The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings – Xinli An – Environmental Science and Pollution Research

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis – Niranjan Nitin Parulekar – PLOS One

Food microbiology

Editorial: Inner Workings: Fermented foods offer up a versatile microbial model system – Alla Katsnelson – PNAS

Probiotics / prebiotics

News article: IBS cure? Probiotics could REDUCE irritable bowel syndrome symptoms AND stress – Olivia Lerche – express.co.uk

 Bioinformatics

Applied Metagenomics for Biofuel Development and Environmental Sustainability – Antonio Djalma Nunes Ferraz Junior – Advances of Basic Science for Second Generation Bioethanol from Sugarcane

DEMOGRAPHICS INDUCE EXTINCTION OF DISEASE IN AN SIS MODEL BASED ON CONDITIONAL MARKOV CHAIN – XIAOFENG LUO – Journal of Biological Systems

Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters – Yu Shang – PLOS One

Techniques

Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods – Beibei Wang – Science of The Total Environment

*How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity – Camille Truong – New Phytologist

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research – Shaocun Zhang – Frontiers in Cellular and Infection Microbiology

Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods

Ed’s non-microbiology picks (news articles)

First Time Ever: Gene Therapy Reverses Sickle Cell Disease

Earth’s oceans are warming 13% faster than thought, and accelerating

MIT researchers create new form of matter

Gene therapy treats muscle-wasting disease in dogs

World’s oldest plant fossil discovered by student pushes evolution of complex life back 400 million years

 

March 9, 2017

A variety of reviews about the oral microbiome and periodontal disease, a perspective piece on secondary metabolites mediating symbiotic interactions in the new Nature Reviews Chemistry journal, Akkermansia muciniphila’s involvement in host immune homeostasis, new insight into how raindrops disperse bacteria from soil into the air.

General microbiome

* Perspective: Hijacking exogenous signals to generate new secondary metabolites during symbiotic interactions – Rurun Wang – Nature Reviews Chemistry

Cooperation of Gastric Mononuclear Phagocytes with Helicobacter pylori during Colonization – Monica Viladomiu – Journal of Immunology

Human respiratory microbiome

Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis – Fiona J. Whelan – PLoS ONE

Human oral microbiome

Review: Role of microbial communities in the pathogenesis of periodontal diseases and caries – Alex Mira – Journal of Clinical Periodontology

Review: Dental biofilm: ecological interactions in health and disease – P. D. Marsh – Journal of Clinical Periodontology

Review: The oral cavity microbiota: between health, oral disease and cancers of the aerodigestive tract – Pierre Le Bars – Canadian Journal of Microbiology

A new mathematical model of bacterial interactions in two-species oral biofilms – Bénédicte Martin – PLoS ONE

Human urinary microbiome

Alterations of Urinary Microbiota in Type 2 Diabetes Mellitus with Hypertension and/or Hyperlipidemia – Fengping Liu – Frontiers in Physiology

Human gut microbiome

Impact of Bariatric Surgery on Metabolic and Gut Microbiota Profile: a Systematic Review and Meta-analysis – Dimitrios E. Magouliotis – Obesity Surgery

Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells – Malgorzata Nepelska – Scientific Reports

* Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function – Noora Ottman – PLoS ONE

Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities – Sai Manasa Jandhyala – Scientific Reports

Disease-Associated Changes in Bile Acid Profiles and Links to Altered Gut Microbiota – Susan A. Joyce – Digestive Diseases

One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents – Alicia Ruiz – Environmental Microbiology

Dysbiosis of Gut Microbiota Associated with Clinical Parameters in Polycystic Ovary Syndrome – Rui Liu – Frontiers in Microbiology

Animal experiments

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat – Elaine Patterson – Scientific Reports

Exploring gastric bacterial community in young pigs – Vincenzo Motta – PLoS ONE

Animal microbiome

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – M. S. Llewellyn – Scientific Reports

The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus – Michelle D. Audsley – PLoS Neglected Tropical Diseases

Endosymbiotic calcifying bacteria across sponge species and oceans – Leire Garate – Scientific Reports

Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials – Jian Zhang – Journal of Marine Systems

Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure – Jasmine J. Hatton – Environmental Microbiology

Plant, root, and soil microbiome

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies – Tomasz Mieczan – Microbial Ecology

Rhizospheric microbial community of Caesalpinia spinosa (Mol.) Kuntze in conserved and deforested zones of the Atiquipa fog forest in Peru – Irene Cordero – Applied Soil Ecology

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland – Yuan He – Canadian Journal of Microbiology

Alphaproteobacteria fix nitrogen in a Sphagnum-dominated peat bog using molybdenum-dependent nitrogenase – Melissa J. Warren – bioRxiv

Water and extremophile microbiome

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem – Yuanqi Wang – Applied and Environmental Microbiology

Comparison of Prokaryotic Diversity in Cold, Oligotrophic Remote Lakes of Chilean Patagonia – Paulina Aguayo – Current Microbiology

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes – Ankita Kothari – bioRxiv

Food microbiology

Characterization of microbial population of breba and main crops (Ficus carica) during cold storage: Influence of passive modified atmospheres (MAP) and antimicrobial extract application – María del Carmen Villalobos – Food Microbiology

Genetic diversity, safety and technological characterization of lactic acid bacteria isolated from artisanal Pico cheese – M. F. P. Domingos-Lopes – Food Microbiology

Probiotics/prebiotics

A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation – Ryo Aoki – Scientific Reports

More microbes

* Bioaerosol generation by raindrops on soil – Young Soo Joung – Nature Communications

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces – Robin Tecon – Scientific Reports

Microbes in the news

The ‘Dark Matter’ of the Microbial World – Sarah Zhang – The Atlantic

Scientists Make Art From Objects Invisible to the Naked Eye – Marissa Fessenden – Smithsonian

March 6, 2017

Interesting articles on the how the interactions between bacteria and fungi influence N cycling in soils. Also, fecal sample collection methods influence microbial community structure.

General microbiome

The National Biome Initiative: An Allergy Perspective. Furuta GT. Journal of Allergy and Clinical Immunology

The Microbiome in Allergic Disease: Current Understanding and Future Opportunities – 2017 PRACTALL Document of the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergy and Clinical Immunology. Huang YJ. Journal of Allergy and Clinical Immunology

Oral and nasal microbiome

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients.      Marino PJ. Journal of Critical Care

Oral and nasal microbiota in Parkinson’s disease. Pereira PA. Parkinsonism and Related Disorders

Gut microbiome

The effect of omeprazole treatment on the gut microflora and neutrophil function. Kostrzewska M. Clinics and Research in Hepatology and Gastroenterology

Water and extremophile microbiome

Bacterial interactions and implications for oil biodegradation process in mangrove sediments. Grativol AD. Marine Pollution Bulletin

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem. Wang Y. Applied and Environmental Microbiology

Probiotics

Probiotic treatment reduces depressive-like behaviour in rats independently of diet. Abildgaard A. Psychoneuroendocrinology

Techniques

Comparison of fecal collection methods for microbiota studies in Bangladesh. Vogtmann E. Applied and Environmental Microbiology

Plant, root, and soil microbiome

How interacting fungal species and mineral nitrogen inputs affect transfer of nitrogen from litter via arbuscular mycorrhizal mycelium. He Y. Environmental Science and Pollution Research

Salmonella Senftenberg adaptation to linalool and its association with antibiotic resistance and environmental persistence. Hollander K. Applied and Environmental Microbiology

Fungal and bacterial contributions to nitrogen cycling in cheatgrass-invaded and uninvaded native sagebrush soils of the western USA.  DeCrappeo NM. Plant and Soil

Native soil organic matter as a decisive factor to determine the arbuscular mycorrhizal fungal community structure in contaminated soils. Montiel-Rozas. Biology and Fertility of Soils

February 24, 2017

Bioassay-guided metabolomics reveal new polyketide macrolactams from termite-associated actinomycete, the microbiota affects host antibody repertoire, artist makes agar molds of her face and grows bacteria on them, the fecal microbiota of Old World vultures.

Events and jobs

“Research Instructor – Microbiology & Immunology” at the Medical University of South Carolina

General microbiome

Review: Carcinogenesis and therapeutics: the microbiota perspective – Matthew C. B. Tsilimigras – Nature Microbiology

Pregnancy and early life

Review: Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period – Xian Chen – American Journal of Reproductive Immunology

Impact of microbial invasion of amniotic cavity and the type of microorganisms on short-term neonatal outcome in women with preterm labor and intact membranes – Teresa Cobo – Acta Obstetricia et Gynecologica Scandinavica

Human oral microbiome

Betel nut chewing, oral premalignant lesions, and the oral microbiome – Brenda Y. Hernandez – PLOS One

Human gut microbiome

Review: Gut Microbiota: A Potential Regulator of Neurodevelopment – Paola Tognini – Frontiers in Cellular Neuroscience

New evidences on the altered gut microbiota in autism spectrum disorders – Francesco Strati – Microbiome

Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman – C. I. Lo – New Microbes and New Infections

Impact of humic acids on the colonic microbiome in healthy volunteers – Alexander Swidsinski – World Journal of Gastroenterology

Animal experiments

IgD class switching is initiated by microbiota and limited to mucosa-associated lymphoid tissue in mice – Jin Huk Choi – PNAS

An Intestinal Farnesoid X Receptor-Ceramide Signaling Axis Modulates Hepatic Gluconeogenesis in Mice – Cen Xie – Diabetes

Effects of xylanase supplementation on growth performance, nutrient digestibility, blood parameters, fecal microbiota, fecal score and fecal noxious gas emission of weaning pigs fed corn-soybean meal-based diet – Ruixia Lan – Animal Science Journal

Animal microbiome

Assessment of Ruminal Bacterial and Archaeal Community Structure in Yak (Bos grunniens) – Zhenming Zhou – Frontiers in Microbiology

Changes in Metabolically Active Bacterial Community during Rumen Development, and Their Alteration by Rhubarb Root Powder Revealed by 16S rRNA Amplicon Sequencing – Zuo Wang – Frontiers in Microbiology

Metataxonomics reveal vultures as a reservoir for Clostridium perfringens – Xiangli Meng – Emerging Microbes and Infections

The fecal microbiome of dogs with exocrine pancreatic insufficiency – Anitha Isaiah – Anaerobe

Plant, root, and soil microbiome

Host-parasite-bacteria triangle: the microbiome of the parasitic weed Phelipanche aegyptiaca and tomato-Solanum lycopersicum (Mill.) as a host – Lilach Iasur Kruh – Frontiers in Plant Science

Diversity of root-associated fungi of Vaccinium mandarinorum along a human disturbance gradient in subtropical forests, China – Yanhua Zhang – Journal of Plant Ecology

Effects of long-term heavy metals contamination on soil microbial characteristics in calcareous agricultural lands (Saiss plain, North Morocco) – A. Kouchou – Journal of Materials and Environmental Sciences

Global transcriptional response to salt shock of the plant microsymbiont Mesorhizobium loti MAFF303099 – Marta Laranjo – Research in Microbiology

Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice – Ramya Krishnan – Research in Microbiology

Assembly patterns of soil-dwelling lichens after glacier retreat in the European Alps – Juri Nascimbene – Journal of Biogeography

Soil classification predicts differences in prokaryotic communities across a range of geographically distant soils once pH is accounted for – Rachel Kaminsky – bioRxiv

Water and extremophile microbiome

Different types of diatom-derived extracellular polymeric substances drive changes in heterotrophic bacterial communities from intertidal sediments – Julio Bohorquez – Frontiers in Microbiology

Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core – Deborah C. A. Leite – Frontiers in Microbiology

Built environment

Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing – Tiago Palladino Delforno – MicrobiologyOpen

Metabolomics

* Macrotermycins A−D, Glycosylated Macrolactams from a Termite- Associated Amycolatopsis sp. M39 – Christine Beemelmanns – Organic Letters

compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets – William Matthew Bell Edmands – Analytical Chemistry

More microbes

Indole production provides limited benefit to Escherichia coli during co-culture with Enterococcus faecalis – Shelly L. Pringle – Archives of Microbiology

Microbes in the news

* Art Grows on You – Lara Medlam – Nouse

Beware! Are bacteria raising your oxidative stress? – Purna Kashyap – Science Translational Medicine

Microbes on the market

Finch Therapeutics Announces Strategic Collaboration with OpenBiome to Develop Microbiome Therapies for FDA Approval – Business Wire

February 23, 2017

Today’s selection includes an interesting review on how bacteria keep their time. Long term ceftriaxon sodium usage alters gut microbiota and immune system. Clostridium perfringens toxin genes in the gut microbiota of autistic children. Taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. Enjoy!

General microbiome

Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status. – Akito Sakanaka – Scientific Reports

*Review: Timing the day: what makes bacterial clocks tick? – Carl Hirschie Johnson – Nature Reviews Microbiology

Human urinary microbiome

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

Review: Questions and challenges associated with studying the microbiome of the urinary tract – Yige Bao – Annals of Translational Medicine

Review: The association between bacteria and urinary stones. – Andrew L. Schwaderer – Annals of Translational Medicine

Human nearly-sterile sites 

The Conserved Phylogeny of Blood Microbiome – Malay Bhattacharyya – Molecular Phylogenetics and Evolution

Human gut microbiome

Review: The gut microbiome in human neurological disease: A review. – Helen Tremlett – Annals of Neurology

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wang – Microbial Pathogenesis

Review: Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome. – Hans C. Arora – Annals of Translational Medicine

*Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system. – Yanjie Guo – Scientific Reports

Note Elies Bik: This study was not performed in humans but in a horrible rat model that can only be qualified as torture. This does not test for depression but for extreme stress. Should not have performed. Proceed with extreme caution. Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics. – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Specific inulin-type fructan fibers protect against autoimmune diabetes by modulating gut immunity, barrier function and microbiota homeostasis. – Kang Chen – Molecular Nutrition and Food Research

Gut microbiota and oxalate homeostasis. – Marguerite Hatch – Annals of Translational Medicine

Tryptophan: A gut microbiota-derived metabolites regulating inflammation. – Lucie Etienne-Mesmin –  World Journal of Gastrointestestinal Pharmacology

*Detection of Clostridium perfringens toxin genes in the gut microbiota of autistic children. – Sydney M. Finegold – Anaerobe

Animal experiments

Butyrate restores HFD induced adaptations in brain function and metabolism in mid-adult obese mice – Ilse A. C. Arnoldussen – International Journal of Obesity

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. – Lucie Etienne-Mesmin – Gut

Animal microbiome

Individual Signatures Define Canine Skin Microbiota Composition and Variability. – Anna Cuscó – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬. – Ines Aline Aschenbrenner – Molecular Ecology

Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change. – Lin Li – Ecology and Evolution

Water and extremophile microbiome

*Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. – Etienne Yergeau – Scientific Reports

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. – Adrienne Narrowe – Environmental Microbiology

Food microbiology

Enhanced Control of Listeria monocytogenes by Enterococcus faecium KE82, a Multiple Enterocin–Producing Strain, in Different Milk Environments. – Elpinki Vandera – Journal of food protection

Probiotics / prebiotics

Review: Probiotics for prevention of urinary stones. – John C. Lieske – Annals of Translational Medicine

Review: Review of the mechanisms of probiotic actions in the prevention of colorectal cancer. – Sandra A. dos Reis – Nutrition Research

Phages and viruses

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses – Lisa Zeigler Allen – mSystems

Microbes in the news 

The Future Of Skin Care: Lotions That Feed Our Microbiome

Collapse of Aztec society linked to catastrophic salmonella outbreak

Smart’ bacteria remodel their genes to infect our intestines

Smallest CRISPR So Far Comes from Food Poisoning Bacteria

Anitha’s non-microbiology picks 

An epigenetics gold rush: new controls for gene expression

Scientists discover 7 ‘Earthlike’ planets orbiting a nearby star