Category Archives: Human oral

March 15, 2018

Posted on by

A few interesting articles in early life human microbiome, plus:
A comparison between Staphylococcus epidermidis commensal and pathogenic lineages from the skin of healthy individuals living in North American and India; A new tool to reconstruct microbial genome-scale metabolic models (GSMMs) from their genome sequence; The seasonal changes in Amazon rainforest soil microbiome are associated with changes in the canopy; A specific class of chemicals secreted by birds modulates their feather microbiome; chronic stress alters gut microbiota and triggers a specific immune response in a mouse model of colitis; and evidence that the short chain fatty acids profile in the gut reflects the impact of dietary fibre on the microbiome using the PolyFermS continuous intestinal fermentation model.

Pregnancy and early life

*Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium – Terhi Tapiainen – Pediatric Research

*Bifidobacterium longum subsp infantis CECT7210 supplemented formula reduces diarrhoea in healthy infants: a randomized controlled trial – Joaquin Escribano – Pediatric Research

*Gut microbiota in adolescents and the association with fatty liver: The EPOCH study – Maggie A Stanislawski – Pediatric Research

Review: Does Dysbiosis in Intestinal Microbiome Plays a Role in Children with Relapsing Idiopathic Nephrotic Syndrome? – Crespo-Salgado J. – American Journal of Nephrology

Gut Microbiota Dysbiosis in Children with Relapsing Idiopathic Nephrotic Syndrome – Tsuji S – American Journal of Nephrology

Human skin microbiome

*Phylogenomic Based Comparative Studies on Indian and American Commensal Staphylococcus epidermidis Isolates – Shikha Sharma – Frontiers in Microbiology

Human oral microbiome

Unusual oral mucosal microbiota after hematopoietic cell transplantation with glycopeptide antibiotics: potential association with pathophysiology of oral mucositis – Misato Muro – Folia Microbiologica

Supragingival and subginival microbiota from patients with poor oral hygiene submitted to radiotherapy for head and neck cancer treatment – Elerson Gaetti-Jardim Jr – Archives of Oral Biology

Human nearly-sterile sites

PrePrint: Transcriptome analysis in whole blood reveals increased microbial 1 diversity in schizophrenia – Loes M Olde Loohuis – bioRxiv

Human gut microbiome

Investigations on the interplays between Schistosoma mansoni, praziquantel and the gut microbiome – Pierre H. H. Schneeberger – Parasites and Vectors

FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects – Williams Turpin – Gut Microbes

Bacterial growth, flow, and mixing shape human gut microbiota density and composition – Markus Arnoldini – Gut Microbes

Complementary effects of cereal and pulse polyphenols and dietary fiber on chronic inflammation and gut health – Joseph M. Awika – Food & Function

Roseburia intestinalis alleviates experimental colitis pathology by inducing anti-inflammatory responses – Zhaohua Shen – Gastroenterology and Hepatology

Targeting gut microbiota in hepatocellular carcinoma: probiotics as a novel therapy – Murphy L. Y. Wan – Hepatobiliary Surgery and Nutrition

Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients – Matthew K. Doherty – mBio

Disruption of the Gut Microbiota With Antibiotics Exacerbates Acute Vascular Rejection
Kevin Rey – Transplantation

Review: Multiple hit infection and autoimmunity: the dysbiotic microbiota–ACPA connection in rheumatoid arthritis – Lazaros I Sakkas – Current Opinion in Rheumatology

*****************************

In vitro experiments

*Understanding the prebiotic potential of different dietary fibers using an in vitro continuous adult fermentation model (PolyFermS) – Sophie A. Poeker – Scientific Reports

Animal experiments

Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka – Cell Reports

Fructose liquid and solid formulations differently affect gut integrity, microbiota composition and related liver toxicity: a comparative in vivo study – Raffaella Mastrocola – Journal of Nutritional Biochemistry

NLRX1 Modulates Immunometabolic Mechanisms Controlling the Host–Gut Microbiota Interactions during Inflammatory Bowel Disease – Andrew Leber – Frontiers in Immunology

Tapering Courses of Oral Vancomycin Induce Persistent Disruption of the Microbiota that Provide Colonization Resistance to Clostridium difficile and Vancomycin-Resistant Enterococci in Mice – Myreen E. Tomas – Antimicrobial Agents and Chemotherapy

The Lung Microbiota of Healthy Mice are Highly Variable, Cluster by Environment, and Reflect Variation in Baseline Lung Innate Immunity – Robert P. Dickson – American Journal of Respiratory and Critical Care Medicine

Interactions between stress and sex in microbial responses within the microbiota-gut-brain axis to stress in a mouse model – Matthew C.B. Tsilimigras – Psychosomatic Medicine

*Chronic stress promotes colitis by disturbing the gut microbiota and triggering immune system response – Xinghua Gao – PNAS

Modulation of inflammatory arthritis by gut microbiota through mucosal inflammation and autoantibody generation – Widian K. Jubair – Arthritis & Rheumatology

Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers – Helen M. Golder

Animal microbiome

Gut microbes limit growth in house sparrow nestlings (Passer domesticus) but not through limitations in digestive capacity – Kevin D. Kohl – Integrative Zoology

*Chemical regulation of body feather microbiota in a wild bird – Staffan Jacob – Molecular Ecology

Plant, root, and soil microbiome

Bacterial community changes in response to oil contamination and perennial crop cultivation – Lijuan Yan – Environmental Science and Pollution Research

Integrated network analysis reveals the importance of microbial interactions for maize growth – Jiemeng Tao – Applied Microbiology and Biotechnology

*Spatio-temporal dynamics of soil bacterial communities as a function of Amazon forest phenology – Erika Buscardo – Scientific Reports

Microbiome dynamics during ensiling of corn with and without Lactobacillus plantarum inoculant – Jitendra Keshridf – Applied Microbiology and Biotechnology

Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture – Linkun Wu – International Journal of Molecular Sciences

Chrysomya megacephala larvae feeding favourably influences manure microbiome, heavy metal stability and greenhouse gas emissions – Xiaoyun Wang – Microbial Biotechnology

Water and extremophile microbiome

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community – Laura Gómez-Consarnau – bioRxiv

Microbial Ecology

Mycotoxin: Its Impact on Gut Health and Microbiota – Winnie-Pui-Pui Liew – Frontiers in Cellular and Infection Microbiology

*****************************

Probiotics / prebiotics

Effect of an Enterococcus faecium probiotic on specific IgA following live Salmonella Enteritidis vaccination of layer chickens – Breno C. B. Beirão – Avian Pathology

Effect of a Protein Supplement on the Gut Microbiota of Endurance Athletes: A Randomized, Controlled, Double-Blind Pilot Study – Diego Moreno-Pérez – Nutrients

Fecal Transplants

Fecal transplants in spondyloarthritis and uveitis: ready for a clinical trial? – Rene Y Choi – Current Opinion in Rheumatology

Phages and viruses

Together Forever: Bacterial–Viral Interactions in Infection and Immunity – Zhenda Shi – Viruses

Bioinformatics

*Towards predicting the environmental metabolome from metagenomics with a mechanistic model – Daniel R. Garza – Nature Microbiology

Phylogenetic convolutional neural networks in metagenomics – Diego Fioravanti – BMC Bioinformatics

Waste and Pollution

Illumina MiSeq Sequencing reveals microbial community in HA process for dyeing wastewater treatment fed with different co-substrates – Xuehui Xie – Chemosphere

Techniques

Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis – Jocelyn Sietsma Penington – Scientific Reports

Direct detection of Coccidioides from Arizona soils using CocciENV, a highly sensitive and specific real-time PCR assay – J R Bowers – Medical Mycology

*****************************

 

March 14, 2018

Posted on by

Today’s Digest adds to the growing literature of microbiome research. Highlights include the synergistic relationship between fungi and an invasive plant, enteral nutrition may help maintain the gastrointestinal function of critically ill patients, and the NCI calls for advancing epidemiologic research on the human microbiome.

Jobs

Student Trainee Microbiology Student Trainee Usda Pathways Internship Program Job in SAINT LOUIS, MO – Opening from 3/12-3/16, 2018

General microbiology

Antibiotic-induced population fluctuations and stochastic clearance of bacteria – Jessica Coates et al. – eLife

Press: Biophysicists discover how small populations of bacteria survive treatment – Science Daily

Preprint: Division of labor during biofilm matrix production – Anna Dragos et al. – bioRxiv

Isolation and characterization of two novel groups of kanamycin-resistance ColE1-like plasmids in Salmonella enterica serotypes from food animals – Chin-Yi Chen et al. – PLoS One

Human nasal microbiome

Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities – Yaqi You et al. – PLoS One

Human oral microbiome

In vitro: pH changes of mixed biofilms of Streptococcus mutans and Candida albicans after exposure to sucrose solutions in vitro – Thamires Priscila Cavazana et al. – Archives of Oral Biology

Human lung microbiome

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis – Lisa A. Carmody et al. – PLoS One

Human gut microbiome

** Review: Effects of enteral nutrition on gastrointestinal function in patients who are critically ill – Michael Schörghuber and Sonja Fruhwald – The Lancet Gastroenterology & Hepatology

An overview on the interplay between nutraceuticals and gut microbiota – Adrian Catinean et al. – PeerJ

Animal experiments

Aronia berry (Aronia mitschurinii ‘Viking’) inhibits colitis in mice and inhibits T cell tumour necrosis factor-α secretion – Derek A. Martin et al. – Journal of Functional Foods

Mouse: Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka et al. – Cell Reports

Animal microbiome

Pathology and bacteria related to digital dermatitis in dairy cattle in all year round grazing system in Brazil – Tiago F. Moreira et al. – PLoS One

Food microbiology

The potential use of leaf extracts of two Newtonia (Fabaceae) species to treat diarrhoea – K.E. Motlhatlego et al. – South African Journal of Botany

Editorial: The interactions between food components and human nutrition – Charles Brennan – International Journal of Food Science & Technology

Plant, root and soil microbiome

** The unspecificity of the relationships between the invasive Pennisetum setaceum and mycorrhizal fungi may provide advantages during its establishment at semiarid Mediterranean sites – G. Rodríguez-Caballero et al. – Science of the Total Environment

Review: Environmental and public health related risk of veterinary zinc in pig production – Using Denmark as an example – John Jensen et al. – Environment International

Hydrophobins contribute to root colonization and stress responses in the rhizosphere-competent insect pathogenic fungus Beauveria bassiana – Soumya Moonjely et al. – Microbiology

Perspective: Tracing the role of human civilization in the globalization of plant pathogens – Alberto Santini et al. – ISME

Water and extremophile microbiome

Review: Surface water flooding, groundwater contamination, and enteric disease in developed countries: A scoping review of connections and consequences – L. Andrade et al. – Environmental Pollution

Domestic wastewater treatment and power generation in continuous flow air-cathode stacked microbial fuel cell: Effect of series and parallel configuration – Edson Baltazar Estrada-Arriaga et al. – Journal of Environmental Management

Effect of particle size and heterogeneity on sediment biofilm metabolism and nutrient uptake scaled using two approaches – Samuel P. Parker et al. – Ecosphere

Phages and viruses

Differential impact of lytic viruses on prokaryotic morphopopulations in a tropical estuarine system (Cochin estuary, India) – Vijayan Jasna et al. – PLoS One

Bioinformatics

A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data – Juhee Lee and Marilou Sison-Mangus – Frontiers in Microbiology

A systems pharmacology model for inflammatory bowel disease – Violeta Balbas-Martinez et al. – PLoS One

Microbes in the news

** Of Microbes and Men: Advancing Epidemiologic Research on the Human Microbiome – Victoria Fisher – National Cancer Institute

Opinion: Inflammatory bowel disease: complexity and variability need integration – Claudio Fiocchi – Frontiers in Medicine

Stress: How social conflict alters gut bacteria – Maria Cohut – Medical News Today

High-Fiber Generates Gut Bacteria Good for Type 2 Diabetes – Becky McCall – Medscape

New pathway may lead to improved probiotic products – Tim Lundeen – Feedstuffs

Probiotic potential: Specific gut microbes could cut severity of parasitic infections in developing countries – Nathan Gray – NUTRAingredients

Wandering Gut Bacteria Could Be Behind Conditions Like Lupus – Abby Norman – Futurism

Model Can Predict Which Bacteria will Engraft after FMT – Rachel Lutz – MD Magazine

Can Coral Microbes Protect Reefs From Climate Change? – Amelia Urry – NewsDeeply

Study: Several important vaginal metabolites elevated in smokers – Bob Kronemyer – Modern Medicine

Doctors collect viruses from pond and employ them to combat a man’s antibiotic resistance infection in man’s heart – Mark Kaufman – Mashable

Making good bacteria more resilient – Gali Weinreb – Globes

Study links decline of ‘good’ bacteria in infants to higher long-term increases in pH of poo – Tim Cutcliffe – NUTRAingredients

Microbes on the market

German biotech company wants to turn old PCs into gold – Jeremy Gray – Handelsblatt Global – European Business & Finance News

 

March 11, 2018

Posted on by

Events and jobs

EVEN seminar: Weakest link in water quality control: Drinking water biofilm in premise plumbing – INSTAAR, CU Boulder

General microbiome

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes – Aura Ferreiro, Cell

Egalitarianism in Biofilms – Dawen Gao, Microbial Ecology

Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds – Hui Wang, Frontiers in Microbiology

Human multi-site microbiome

The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis – Raphaël Enaud, Microorganisms

Human gut microbiome

Gut Microbiota Alteration After Long-Term Consumption of Probiotics in the Elderly – Renyuan Gao, Probiotics and Antimicrobial Proteins

Sex differences in gut microbiota in patients with major depressive disorder – Chen JJ, Neuropsychiatric Disease and Treatment

Oral microbiome

Influence of periodontal treatment on subgingival and salivary microbiotas – Daniel Belstrøm, Journal of Periodontology

Microbiome at sites of gingival recession in children with Hutchinson–Gilford progeria syndrome – Seyed Hossein Bassir, Journal of Periodontology

Subgingival microbial profile of obese women with periodontal disease – Carina M. Silva-Boghossian, Journal of Periodontology

Animal experiments

The effect of probiotics and polysaccharides on the gut microbiota composition and function of weaned rats – Mengxia Wang, Food and Function

Cecal Versus Fecal Microbiota in Ossabaw Swine and Implications for Obesity – Matthew R Panasevich, Physiological Genomics

Antibiotics-induced modulation of large intestinal microbiota altered aromatic amino acid profile and expression of neurotransmitters in the hypothalamus of piglets – Kan Gao, Journal of Neurochemistry

Animal microbiome

Nutrient factories: Metabolic function of beneficial microorganisms associated with insects – Nana Y. D. Ankrah, Environmental Microbiology

Community composition, diversity, and metabolism of intestinal microbiota in cultivated European eel (Anguilla anguilla) – Wei Huang, Applied Microbiology and Biotechnology

Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs – Brandon J. Varela, Frontiers in Microbiology

Influence of Novel Highly Pathogenic Avian Influenza A (H5N1) Virus Infection on Migrating Whooper Swans Fecal Microbiota – Na Zhao, Frontiers in Cellular and Infectious Microbiology

Plant, root, and soil microbiome

The Soil-Borne Legacy – Peter A.H.M. Bakker, Cell

Water and extremophile microbiome

Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic – Omar Federico Ordoñez, Microbial Ecology

Occurrence of Legionella in Nonpotable Reclaimed Water – William J. Johnson, American Water Works Association

Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi’an, China – Haihan Zhang, International Journal of Environmental Research and Public Health

Food microbiome

Microbial community and physicochemical dynamics during the production of ‘Chicha’, a traditional beverage of Indigenous people of Brazil – Ludmila Vilela Resende, World Journal of Microbiology and Biotechnology

Techniques

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton – Emma K. Wear, Environmental Microbiology

Microbes in the news

Pitting Viruses Against Bacteria To Combat The Antibiotic Crisis – SciFri

March 9, 2018

Posted on by

Have a nice Friday! Today we have interesting papers about nasal/oral microbiota, some papers about studies in pathogens (including the use of bacteriophages for selective inhibition of E. coli), DNA extraction studies in meconium, and more!

 

Human/General Microbiome

Review: Microbiota metabolites: Pivotal players of cardiovascular damage in chronic kidney disease – Carmela Cosola – Pharmacological Research

Predictive biomarkers for type 2 of diabetes mellitus: bridging the gap between systems research and personalized medicine – Christina Kraniotou – Journal of Proteomics

The Nasal Microbiome in Asthma – Mina Fazlollahi – Journal of Allergy and Clinical Immunology

Metatranscriptome of the Oral Microbiome in Health and Disease – J. Solbiati – Journal of Dental Research

Nasal Microbiota and Respiratory Tract Infections: The Role of Viral Detection – Insa Korten – American Journal of Respiratory and Critical Care Medicine

Short term dynamics of the sputum microbiome among COPD patients – Rohita Sinha – Plos One

The effect of medical treatments on the bacterial microbiome in patients with chronic rhinosinusitis: a pilot study – Ravi Jain – International Forum of Allergy & Rhinology

The Influence of Cervicovaginal Microbiota on Mucosal Immunity and Prophylaxis in the Battle against HIV – Mara Farcasanu – Current HIV/AIDS Reports

Emerging Mechanisms of Innate Immunity and Their Translational Potential in Inflammatory Bowel Disease – Daniele Corridoni – Frontiers in Medicine

Oropharyngeal Microbiota in Frail Older Patients Unaffected by Time in Hospital – Victoria C. Ewan – Frontiers In Cellular And Infection Microbiology

Influence of Intestinal Indigenous Microbiota on Intrafamilial Infection by Helicobacter pylori in Japan – Takako Osaki – Frontiers in Immunology

Comparison of Meconium DNA Extraction Methods for Use in Microbiome Studies – Lisa F. Stinson – Frontiers in Microbiology

Minireview: Gut Microbiota: An Integral Moderator in Health and Disease – Qingqing Feng –   Frontiers in Microbiology

Activation of Notch-1 in oral epithelial cells by P. gingivalis triggers the expression of the antimicrobial protein PLA2-IIA – Ahmad Al-Attar – Mucosal Immunology

Gut microbial RNA and DNA analysis predicts hospitalizations in cirrhosis – Jasmohan S. Bajaj –  JCI Insight

Physiological Regulation of Drug Metabolism and Transport: Pregnancy, Microbiome, Inflammation, Infection, and Fasting – Edward T. Morgan – Drug Metabolism and Disposition

 

Pathogen Research

A bacteriophage cocktail targeting Escherichia coli reduces E. coli in simulated gut conditions, while preserving a non-targeted representative commensal normal microbiota – Tomasz Cieplak – Gut Microbes

Triclosan Enhances the Clearing of Pathogenic Intracellular Salmonella or Candida albicans but Disturbs the Intestinal Microbiota through mTOR-Independent Autophagy – Chao Wang – Frontiers In Cellular And Infection Microbiology

The Metabolic Sensor GPR43 Receptor Plays a Role in the Control of Klebsiella pneumoniae Infection in the Lung – Izabela Galvão – Frontiers in Immunology

Parasite-Vector Interaction of Chagas Disease: A Mini-Review – Ana Beatriz Bortolozo de Oliveira – The American Journal of Tropical Medicine and Hygiene – Current Issue

Bacillus subtilis spore with surface display of paramyosin from Clonorchis sinensis potentializes a promising oral vaccine candidate – Hengchang Sun – Parasites & Vectors

 

Animal Microbiome

Instar- and host-associated differentiation of bacterial communities in the Mediterranean fruit fly Ceratitis capitata – Antonino Malacrinò – Plos One

Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates – Tasha Barr – Gut Microbes

Integrating molecular and ecological approaches to identify potential polymicrobial pathogens over a shrimp disease progression – Wenfang Dai – Applied Microbiology And Biotechnology

Intestinal bacterial signatures of white feces syndrome in shrimp – Dongwei Hou – Applied Microbiology And Biotechnology

Bile acid metabolism regulated by the gut microbiota promotes non-alcoholic steatohepatitis-associated hepatocellular carcinoma in mice – Shoji Yamada – Oncotarget

Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila – Fumiaki Obata – Nature Communications

Physiological mechanisms of sustained fumagillin-induced weight loss – Jie An – JCI Insight

Gpr109a Limits Microbiota-Induced IL-23 Production To Constrain ILC3-Mediated Colonic Inflammation – Brinda Bhatt – The Journal in Immunology

Fuzhuan brick tea polysaccharides attenuate metabolic syndrome in high-fat diet induced mice in association with modulation in the gut microbiota – Guijie Chen – Journal Of Agricultural And Food Chemistry

 

Extremophiles

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) – Blanca Vera-Gargallo – Genes

 

Plant Microbiome

Disease-induced assemblage of a plant-beneficial bacterial consortium – Roeland L. Berendsen – The ISME Journal

March 8, 2018

Posted on by

A wide range of interesting articles today: the use of fungi communities in the production of gold nanoparticles, a link between dysbiosis of the oral microbiome and rheumatoid arthritis, a diet low in PKU decreases fecal butyrate, the bacterial diet of  C. elegans alters their proteome, and a functional metagenomic study of the gut microbiome of the giant panda.

Events and jobs

Postdoctoral Associate – School of Medicine/Surgery – University of Pittsburgh Health Sciences

*****************************

General microbiome

Review: Understanding the microbiome – Mark Buchanan – Nature Physics

Pregnancy and early life

Conference Proceedings: Biology and Science of Human Milk – Integrated Approaches to Analyze Big Data in the Perinatal/Neonatal Space – Rob Knight – Human Milk Science

PrePrint: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T. Brown – bioRxiv

Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis – Martin Glatz – PLOSone

Human oral microbiome

*Dysbiotic subgingival microbial communities in periodontally healthy patients with rheumatoid arthritis – Isabel Lopez-Oliva – Arthritis and Rheumatology

Human gut microbiome

*Phenylketonuric diet negatively impacts on butyrate production – E. Verduci – Nutrition, Metabolism and Cardiovascular Diseases

Review: Microbiotes et rhumatismes inflammatoires – Matthias Jarlborg – Revue Medicale Suisse

Gut Microbiome Composition Predicts Infection Risk during Chemotherapy in Children with Acute Lymphoblastic Leukemia – Hana Hakim – Clinical Infectious Diseases

PrePrint: American Gut: an Open Platform for Citizen-Science Microbiome Research – Daniel McDonald – bioRxiv

Review: Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis: a role for bifidobacteria and lactobacilli? – Borja Sánchez – Gastroenterology and Hepatology

*****************************

Animal microbiome

Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls – Zhenming Zhou – Applied Microbiology and Biotechnology

*Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda (Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation – Wei Guo – Frontiers in Microbiology

*The C. elegans Proteome Response to Naturally Associated Microbiome Members of the Genus Ochrobactrum – Liam Cassidy – Proteomics

16S rRNA gene sequencing reveals effects of photoperiod on cecal microbiota of broiler roosters – Jun Wang – PeerJ

The Drosophila melanogaster Gut Microbiota Provisions Thiamine to Its Host – David R. Sannino – mBio

Host and aquatic environment shape the amphibian skin microbiome but effects on downstream resistance to the pathogen Batrachochytrium dendrobatidis are variable – Andrea J. Jani – Frontiers in Microbiology

A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach – Sarayu Bhogoju – PLOSone

Plant, root, and soil microbiome

Impact of wastewater effluent containing aged nanoparticles and other components on biological activities of the soil microbiome, Arabidopsis plants, and earthworms – Jia Liu – Environmental Research

Dissertation: The influence of intraspecific variation in host plants on arthropod and fungal endophyte communities – Joshua G. Harrison – University of Nevada

Soil Microbiology Research in the Coming Decades: Translational Research Opportunities – Tapan Kumar Adhya – Advances in Soil Microbiology: Recent Trends and Future Prospects

Divergence of dominant factors in soil microbial communities and
functions in forest ecosystems along a climatic gradient – Zhiwei Xu – Biogeosciences

Climate, but not trait, effects on plant–soil feedback depend on mycorrhizal type in temperate forests – Jonathan A. Bennett – Ecosphere

Arbuscular Mycorrhiza Alleviates Restrictions to Substrate Water Flow and Delays Transpiration Limitation to Stronger Drought in Tomato – Michael Bitterlich – Frontiers in Plant Science

Ecological responses to forest age, habitat, and host vary by mycorrhizal type in boreal peatlands – Peter G. Kennedy – Mycorrhiza

Microbial Ecology

Holobionts and their hologenomes: Evolution with mixed modes of inheritance – Karen Luisa Haag – Genetics and Molecular Biology

Resistome

PrePrint: Conjugation factors controlling F-plasmid antibiotic resistance transmission – Hanna Alalam – bioRxiv

Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense – Malcolm James Horsburgh – bioRxiv

Bioinformatics

PrePrint: MetaWRAP – a flexible pipeline for genome-resolved metagenomic data analysis
– Gherman V Uritskiy – bioRxiv

Biotechnology

*Green synthesis of gold nanoparticles by thermophilic filamentous fungi – Zsófia Molnár – Scientific Reports

Techniques

Evaluation of magnetic cellulose bead-based DNA extraction from faecal materials for high-throughput bacterial community analyses – Tanzila Afrin – Applied Entomology and Zoology

*****************************

Microbes in the news

How extremophiles flourish in stressful environments – Science Daily

Does a Microbiome Exist in the Womb? – Medical News Bulletin

IBS and the Developing Microbiome – David Carreon – Modern Medicine Network

Bacteria and Art

Finding Art in the Gut, and Other Unexpected Places – Patrician Olsen – The New York Times

This Psychedelic Art Made from Moldy Food Is Tripping Us Out – Artist Felix Kalmenson proves decay can be gorgeous – Anna Marks – Vice

Artist to offer presentation on ‘Living Light’ exhibit March 5 at MCC – Daily Herald

March 6, 2018

Posted on by

In today’s digest we have many interesting articles, particularly in “General Microbiome” section. Check a review on integrative view of cell cycle control in E. coli by L. Dewachter, an article on the return of cultures in microbiology by V. Marx, an article on microbial altruism and cheating in social amoebas by S. Noh. Don’t miss great articles from other sections, like “Water microbiome” where I would recommend an article deciphering the evolution and metabolism of an anammox bacterium by M. Strous and an article about globally overlooked nanoplanktonic diatoms by K. Leblanc. Happy reading!

Events

The Human Microbiome, EMBL Heidelberg, Germany, 16 – 19 Sep 2018

Jobs

Qc Analyst- Microbiology, Liverpool, UK

General microbiome

Commensal Koch’s postulates: establishing causation in human microbiota research – Anne Neville – Current Opinion in Microbiology

Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect routes – Grace M. Kroner – bioRxiv

Review: An integrative view of cell cycle control in Escherichia coli – Liselot Dewachter – FEMS Microbiology Reviews

[Section Head] is Ravdin Lecture in the Basic and Surgical Sciences Microbiome Medicine: This Changes Everything  – John C. Alverdy – Journal of the American College of Surgeons

Regulation of Allergic Immune Responses by Microbial Metabolites – Hyun Jung Park – Immune Network

Microbiology: the return of culture – Vivien Marx – Nature Methods

Review: Bacterial microcompartments – Cheryl A. Kerfeld – Nature Reviews Microbiology

Proposal of the suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes’ – William B. Whitman – International Journal of Systematic and Evolutionary Microbiology

Genetic signatures of microbial altruism and cheating in social amoebas in the wild – Suegene Noh – PNAS

The use of SWATH to analyse the dynamic changes of bacterial proteome of carbapanemase-producing Escherichia coli under antibiotic pressure – Hanna E. Sidjabat – Scientific Reports

Pregnancy and early life

Early fecal microbiota composition in children who later develop celiac disease and associated autoimmunity – Anniina Rintala – Scandinavian Journal of Gastroenterology

Human oral microbiome

Eliminating bias and accelerating the clinical translation of oral microbiome research in oral oncology – Rohit Kunnath Menon  – Oral Oncology

Acid-resistant genes of oral plaque microbiome from the functional metagenomics – Meng Zhang – Journal of Oral Microbiology

Oral microbiota in autoimmune polyendocrine syndrome type 1 – Øyvind Bruserud – Journal of Oral Microbiology

Human vaginal microbiome

Impact of contraceptive initiation on vaginal microbiota  – Sharon L. Achilles – American Journal of Obstetrics and Gynecology

Human gut microbiome

Gut Microbiome Composition Predicts Infection Risk during Chemotherapy in Children with Acute Lymphoblastic Leukemia – Hana Hakim – Clinical Infectious Diseases

Review: Flavonoid metabolism: the interaction of metabolites and gut microbiota – Kaeko Murota – Bioscience, Biotechnology, and Biochemistry

Data Descriptor: Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection – Dominik Schneider – Scientific Data

Animal experiments 

Dietary Tryptophan Restriction Dose-Dependently Modulates Energy Balance, Gut Hormones, and Microbiota in Obesity-Prone Rats – Rizaldy C. Zapata – Obesity

Prevalence of microorganisms associated with feline gingivostomatitis – Hitoshi Nakanishi – Journal of Feline Medicine and Surgery

Effects of Rubus coreanus byproducts on intestinal microbiota and the immune modulation – Da Yoon Yu – Asian-Australasian Journal of Animal Sciences (AJAS)

Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens – Jannigje G. Kers – Frontiers in Microbiology

Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls – Zhenming Zhou – Applied Microbiology and Biotechnology

Animal microbiome 

Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda (Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation – Wei Guo – Frontiers in Microbiology

Plant, root, and soil microbiome

Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient – Jackson W Sorensen – bioRxiv

Phyllosphere microbiology: at the interface between microbial individuals and the plant host – Mitja N. P. Remus-Emsermann – New Phtyologist

Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of “Hidden” Diversity – David Bass – Frontiers in Microbiology

Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China – Tatiana A. Vishnivetskaya – Environmental Science: Processes & Impacts

Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents – Raúl Ochoa-Hueso – Global Change Biology

Temporal succession of soil antibiotic resistance genes following application of swine, cattle and poultry manures spiked with or without antibiotics – Yu-Jing Zhang – Environmental Pollution

Water and extremophile microbiome 

Light-dependent processes on the cathode enhance the electrical outputs of sediment microbial fuel cells – Ivo Bardarov – Bioelectrochemistry

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile – Jeanett Vera – World Journal of Microbiology and Biotechnology

Stepwise impact of urban wastewater treatment on the bacterial community structure, antibiotic contents, and prevalence of antimicrobial resistance – Mingyu Wang – Environmental Pollution

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export – Karine Leblanc – Nature Communications

A novel genus of the class Actinobacteria, Longivirga aurantiaca gen. nov., sp. nov., isolated from lake sediment – Jian-Hang Qu – International Journal of Systematic and Evolutionary Microbiology

Desulfothermobacter acidiphilus gen. nov., sp. nov., a thermoacidophilic sulfate-reducing bacterium isolated from a terrestrial hot spring –  E. N. Frolov – International Journal of Systematic and Evolutionary Microbiology

Deciphering the evolution and metabolism of an anammox bacterium from a community genome – Marc Strous –  Nature

Food microbiology

Dynamics of biofilm formation by Listeria monocytogenes on stainless steel under mono-species and mixed-culture simulated fish processing conditions and chemical disinfection challenges – Eleni Papaioannou – International Journal of Food Microbiology

Probiotics / prebiotics

Novel consortium of Klebsiella variicola and Lactobacillus species enhances the functional potential of fermented dairy products by increasing the availability of branched-chain amino acids and the amount of distinctive volatiles – H. Rosales-Bravo – Journal of Applied Microbiology

Bioinformatics

Updating the 97% identity threshold for 16S‌ ribosomal RNA OTUs – Robert C Edgar – Bioinformatics

Biotechnology

Selection and characterization of an anaerobic microbial consortium with high adaptation to crude glycerol for 1,3-propanediol production – Jin-Jie Zhou – Applied Microbiology and Biotechnology

Microbes in the news

Studying how tiny microbes thrive in harsh environments could lead to better treatments for human diseases

Microbes on the market 

FDA fast-tracks Finch’s microbiome capsule for C. difficile

Science, publishing, and career 

Uniting science and stories: Perspectives on the value of storytelling for communicating science

New round of science journalism projects awarded

 

March 3, 2017

Posted on by

Antiphage defense systems in microbial genomes, oral pathogen inhibition by wine polyphenols and an oral probiotic, and analysis of E. coli gene expression in simulated spaceflight.

Events and jobs

Call for Expressions of Interest: Microbiology Twitter Teachers for New MOOC – Spanish Society for Microbiology

Endowed Chair in Molecular Genetics Waksman Institute of Microbiology – Rutgers University

General microbiome

Creating a 3D microbial and chemical snapshot of a human habitat – Clifford A Kapono – Scientific Reports

Human oral microbiome

Inhibition of Oral Pathogens Adhesion to Human Gingival Fibroblasts by Wine Polyphenols Alone and in Combination with an Oral Probiotic – Adelaida Esteban-Fernández – Journal of Agricultural and Food Chemistry

Human vaginal microbiome

Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Zhi-Luo Deng – bioRxiv

Human gut microbiome

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A Rosa – Microbiome

Animal experiments

Pre-print: Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal – Sean M Kearney – bioRxiv

Pre-print: Clearing the FoG: Antifungal tolerance is a subpopulation effect that is distinct from resistance and is associated with persistent candidemia – Alexander Rosenberg – bioRxiv

Blueberry Supplementation Influences the Gut Microbiota, Inflammation, and Insulin Resistance in High-Fat-Diet–Fed Rats – Sunhye Lee – Journal of Nutrition

Animal microbiome

Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus – Biao Chen – AMB Express

Water and extremophile microbiome

Pre-print: Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom – Rasmus Swalethorp – bioRxiv

Microbes in space

Pre-print: Analysis of Escherichia coli Flagellin Gene Expression in Simulated Spaceflight Growth Conditions – Kyle M Hetrick – bioRxiv

Phages and viruses

Systematic discovery of antiphage defense systems in the microbial pangenome – Shany Doron – Science

Bioinformatics

Pre-print: VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma – Atlas Khan – bioRxiv

Techniques

Pre-print: Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets – Edouard A Hay – bioRxiv

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem – Stilianos Louca – Microbiome

Improving saliva shotgun metagenomics by chemical host DNA depletion – Clarisse A Marotz – Microbiome

Microbes in the news

Your skin is crawling with bacteria, and some of them might help fight cancer – Claire Maldarelli – Popular Science

Most Viruses And Bacteria Fall From The Sky – Astrobiology Web

Microbes on the market

Six Leading Pharma Firms to Participate at Pharmaceutical Microbiology Event in San Diego – Technology Networks

Science, career, and publishing

Pre-print: Persistent Underrepresentation of Women’s Science in High Profile Journals – Yiqin Alicia Shen – bioRxiv

Pre-print: Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist – Holly O Witteman – bioRxiv

February 28, 2018

Posted on by

Have a good Wednesday! After few days of inactivity, we bring this digest with several reviews from different aspects of microbiome research. We included also some papers about microbiota and antibiotic resistance, microbiota and metabolism, and more.

 

Human and General microbiome

Review: Microbiota and Metabolism — What’s New in 2018 – Alexis Bretin – American Journal of Physiology-Endocrinology and Metabolism

Review: Eicosanoids in the GI Tract – John L Wallace – British Journal of Pharmacology

Review: Gut : liver : brain axis: the microbial challenge in the hepatic encephalopathy – Andrea Mancini – Food and Function

Meeting update: faecal microbiota transplantation–bench, bedside, courtroom? – Nik Sheng Ding – . Frontline Gastroenterology

Mini-Review: Involvement of Corticotropin-Releasing Factor and Receptors in Immune Cells in Irritable Bowel Syndrome – Mahanand Chatoo – Frontiers in Endocrinology

Gut microbiome composition in lean patients with NASH is associated with liver damage independent of caloric intake: A prospective pilot study – S.M.B.Duarte – Nutrition, Metabolism and Cardiovascular Diseases

Study protocol: Antifibrotic and molecular aspects of rifaximin in alcoholic liver disease: study protocol for a randomized controlled trial – Bjørn Stæhr Madsen – Trials

Gut microbiota characterisation in obese patients before and after bariatric surgery – G. Campisciano – Beneficial Microbes

Effect of sodium fluoride on oral biofilm microbiota and enamel demineralization – Thomas Thurnheer – Archives of Oral Biology

Review: Human Gut Microbiota in Health and Alzheimer’s Disease – Leszek Szablewski –  Journal of Alzheimer’s Disease

Fecal microbiota profile in atopic asthmatic adult patients – A.M. Okba – European annals of allergy and clinical immunology

Cervicovaginal microbiota composition correlates with the acquisition of high-risk human papillomavirus types – Xiaojie Huang – International journal of cancer

Review: Dysbiosis of gut microbiota in promoting the development of colorectal cancer – Shaomin Zou – Gastroenterology Report

In Brief: Microbiome: Principles of microbiota engraftment – Andrea Du Toit – Nature Reviews Microbiology

Clearance of Carbapenem-resistant Enterobacteriaceae versus Vancomycin-resistant enterococci carriage after fecal microbiota transplant: a prospective comparative study – Aurélien Dinh – The Journal of Hospital Infection

Alterations of the human gut Methanobrevibacter smithii as a biomarker for inflammatory bowel diseases – Shaghayegh Baradaran Ghavami – Microbial Pathogenesis

Forum: Inadequate Production of H2 by Gut Microbiota and Parkinson Disease – Sergej M.Ostojic – Trends in endocrinology and metabolism

Review: Brain Feeding Circuits after Roux-en-Y Gastric Bypass – Mohammed K.Hankir – Trends in endocrinology and metabolism

Temporal variability of oral microbiota over 10 months and the implications for future epidemiologic studies – Emily Vogtmann – Cancer Epidemiology, Biomarkers & Prevention

Review: Psoriatic arthritis: tissue-directed inflammation? – Giacomo Cafaro – Clinical Rheumatology

 

Animal Microbiome

Intestine farnesoid X receptor agonist and the gut microbiota activate G-protein bile acid receptor-1 signaling to improve metabolism – Preeti Pathak – Hepatology

Primary murine mucosal response during cephalosporin-induced intestinal colonization by Enterococcus faecium – Antoni P. A. Hendrickx – MicrobiologyOpen

Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota – Helen T. Groves – Frontiers in Immunology

Tartary buckwheat protein prevented dyslipidemia in high-fat diet-fed mice associated with gut microbiota changes – Xiao-Li Zhou – Food and chemical toxicology

When Darwin’s Special Difficulty Promotes Diversification in Insects – Frederic Legendre – Systematic Biology

Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis – Joel R.Wilmore – Cell host and microbe

Brain-derived neurotrophic factor preserves intestinal mucosal barrier function and alters gut microbiota in mice – Chen Li – The Kaohsiung Journal of Medical Sciences

Microbiota-mediated modulation of organophosphate insecticide toxicity by species-dependent lactobacilli interactions in a Drosophila melanogaster insect model – Brendan A. Daisley – Applied And Environmental Microbiology

Assessing bacterial community dynamics across the gastrointestinal tract of dairy calves during pre-weaning development – Juliana Dias – Applied And Environmental Microbiology

Microbial community dynamics during rearing of black soldier fly larvae (Hermetia illucens) and its impact on exploitation potential – Jeroen De Smet – Applied And Environmental Microbiology

Microbiota promote secretory cell determination in the intestinal epithelium by modulating host Notch signaling – Joshua V. Troll – Development

Hypoglycemic and hypolipidemic effect of S-allyl-cysteine sulfoxide (alliin) in DIO mice – Baiqiang Zhai – Scientific Reports

 

Pathogen research

Immunization with intestinal microbiota-derived Staphylococcus aureus and Escherichia coli reduces bacteria-specific recolonization of the intestinal tract – Julio Adrián Garfias-López – Immunology Letters

Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut – Jikang Wu – Infection and immunity

Treatment of Clostridium difficile infection with a small molecule inhibitor of toxin UDP-glucose hydrolysis activity – Ilana L. Stroke – Antimicrobial agents and chemotherapy

Review: Treatment of recurrent Clostridium difficile colitis: a narrative review – Roy J Hopkins – Gastroenterology Report

Review: Pseudomonas syringae: what it takes to be a pathogen – Xiu-Fang Xin – Nature Reviews Microbiology

 

Food Microbiome

Review: Seafood spoilage microbiota and associated volatile organic compounds at different storage temperatures and packaging conditions – Olumide A.Odeyemi – International journal of food microbiology

 

Water Microbiome

A closer look at the antibiotic-resistant bacterial community found in urban wastewater treatment systems – Amir H. Tehrani – MicrobiologyOpen

 

Extremophiles

Transitory microbial habitat in the hyperarid Atacama Desert – Dirk Schulze-Makuch – PNAS

 

Other papers

Microbial diversity in biodeteriorated Greek historical documents dating back to the 19th and 20th century: A case study – Kiriaki Karakasidou – MicrobiologyOpen

A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses – Mo Han – Microbiome

Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum – Julen Tomás-Cortázar – Microbial Cell Factories

Effect of Bacillus subtilis C-3102 on loose stools in healthy volunteers – M. Hatanaka – Beneficial Microbes

In situ biomolecule production by bacteria; a synthetic biology approach to medicine – Yensi Flores Bueso – Journal of Controlled Release

February 22, 2018

Posted on by

 

Events and jobs

Microbiology Adjunct Instructor – Diablo Valley College

*****************************

Pregnancy and early life

Review: Maternal Microbiota, Prepregnancy Weight, and Mode of Delivery
Intergenerational Transmission of Risk for Childhood Overweight and Obesity – Giulia Paolella – JAMA Pediatrics

 

Human ear, nose and throat microbiome

*A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera – Rachael Lappan – BMC Microbiology

The Tracheal Microbiota in Patients with a Tracheostomy Before, During, and After an Acute Respiratory Infection – Pérez-Losada, Marcos – The Pediatric Infectious Disease Journal

Human oral microbiome

Shift of microbial composition of peri-implantitis-associated oral biofilm as revealed by 16S rRNA gene cloning – Ali Al-Ahmad – Journal of Medical Microbiology

Human vaginal microbiome

Short- and long-term influence of the levonorgestrel-releasing intrauterine system (Mirena®) on vaginal microbiota and Candida – Gilbert Gerard Ghislain Donders – Journal of Medical Microbiology

Human gut microbiome

Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn’s disease of the terminal ileum – Rodrick J. Chiodini – Journal of Medical Microbiology

Gut microbiota trajectory in early life may predict development of celiac disease – Marta Olivares – BMC Microbiome

A comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis – Atsushi Hirano – Journal of Gastroenterology and Hepatology

The Impact of NOD2 Variants on Fecal Microbiota in Crohn’s Disease and Controls Without Gastrointestinal Disease – Nicholas A Kennedy – Inflammatory Bowel Diseases

*****************************

Animal experiments

Regulation of vitamin D metabolism following disruption of the microbiota using broad spectrum antibiotics – Stephanie A. Bora – The Journal of Nutritional Biochemistry

Soluble dietary fiber improves energy homeostasis in obese mice by remodeling the gut microbiota – Haiyuan Wang – Biochemical and Biophysical Research Communications

Lactobacillus and Bifidobacterium Ameliorate Memory and Learning Deficits and oxidative stress in Aβ (1-42) Injected Rats – Somayeh Athari Nik Azm – Applied Physiology, Nutrition, and Metabolism

*Chronic helminth infection perturbs the gut-brain axis, promotes neuropathology and alters behaviour – Paul R Giacomin – The Journal of Infectious Diseases

*Endometriosis induces gut microbiota alterations in mice – Ming Yuan – Human Reproduction

*Strain differences in the susceptibility to the gut–brain axis and neurobehavioural alterations induced by maternal immune activation in mice – Morais, Livia H – Behavioural Pharmacology

Specific synbiotics in early life protect against diet-induced obesity in adult mice
Mona Mischke – Diabetes, Obesity, and Metabolism

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse – Barbora Kuntová – Frontiers in Genetics

Lactobacillus accelerates ISCs regeneration to protect the integrity of intestinal mucosa through activation of STAT3 signaling pathway induced by LPLs secretion of IL-22 – Qihang Hou – Cell Death and Differentiation

Animal microbiome

Review: Gut barrier function: Effects of (antibiotic) growth promoters on key barrier components and associations with growth performance – Leon J Broom – Poultry Science

Fecal microbiota transplantation in puppies with canine parvovirus infection – Giorgio Q. Pereira – Journal of Veterinary Internal Medicine

Water and extremophile microbiome

Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae – Pamela Alvarado – Antonie van Leeuwenhoek

 

Resistome

The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany – Robert Häsler – BMC Microbiome

Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium – François Lebreton – Journal of Antimicrobial Chemotherapy

 

Bioinformatics

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach – Loo Wee Chia – Antonie van Leeuwenhoek

Biotechnology

*A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage – Lamyaa Shaban – Anaerobe

Design of synthetic bacterial communities for predictable plant phenotypes – Sur Herrera Paredes – PLOS Biology

Harnessing a Methane-Fueled, Sediment-Free Mixed Microbial Community for Utilization of Distributed Sources of Natural Gas – Jeffrey J. Marlow – Biotechnology and Bioengineering

Dissertation: Microbial Communities Involved in Carbon Monoxide and Syngas Conversion to Biofuels and Chemicals – Sofia Victoria Esquivel Elizondo – Arizona State University

 

*****************************

Microbes in the news

This Vibrant Bacteria Could Be Used to “Grow” Paint – Meilan Solly – Smithsonian

Bacteria-eaters to prevent food poisoning? Phages eliminate Yersinia from food – Science Daily

A ‘Grueling and Grotesque’ Biohacking Experiment – Kate McLean – The Atlantic

 

February 20, 2018

Posted on by

In today’s digest you can read: about advantages of Atomic Force Microscopy in studying of oral microbiota in the paper by S. S. Salavadhi; about gut microbiome association with Type 1 diabetes in the paper by J.A. Mullaney; about influence of steroids on the gut microbiota in the review by M.J Tetel and about the ability of Synechococcus cyanobacteria to dynamically change their pigment content to match the ambient light color, in the paper by T. Grébert. These are of course just a few of many interesting articles today. Enjoy!

Events and jobs

MS graduate position: Amoeba microbiome, Conway, Arkansas, US

Research Fellow in Cell Biology – Microscopy, Warwick, UK

PhD Student, ROYAL NIOZ-TEXEL, Texel, the Netherlands

General microbiome

Review: A new piece in the microbiome puzzle – Lindsay J. Pike – Nature Reviews Microbiology

The importance of resolving biogeographic patterns of microbial microdiversity – Alexander B Chase – Microbiology Australia

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession – Rüdiger Ortiz-Álvarez – the ISME Journal

Pregnancy and early life

Infant formulae supplemented with prebiotics: Are they better than unsupplemented formulae? An updated systematic review – Agata Skórka – British Journal of Nutrition

Early Dietary Patterns and Microbiota Development: Still a Way to Go from Descriptive Interactions to Health-Relevant Solutions – Patricia Iozzo – Frontiers in Nutrition

Roles of Birth Mode and Infant Gut Microbiota in Intergenerational Transmission of Overweight and Obesity From Mother to Offspring – Hein M. Tun – JAMA Pediatrics

Multi-site human microbiome

A blinded observational cohort study of the microbiological ecology associated with pyuria and overactive bladder symptoms – Kiren Gill – International Urogynecology Journal

Oral microbiome

Atomic force microscopy: A three-dimensional reconstructive tool of oral microbiota in gingivitis and periodontitis – Shyam Sunder Salavadhi – Journal of Indian Society of Periodontology

Human gut microbiome

Review: Steroids, stress and the gut microbiome-brain axis – M. J. Tetel – Journal of Neuroendocrinology

Alterations of the Gut Microbiota in Hashimoto’s Thyroiditis Patients – Zhao Fuya – Thyroid

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean Michael Kearney – bioRxiv

Alterations in Intestinal Microbiota Lead to Production of Interleukin 17 by Intrahepatic γδ T-cell Receptor-positive Cells and Pathogenesis of Cholestatic Liver Disease – Dana Tedesco – Gastroenterology

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota – Jane A. Mullaney – BMC Microbiome

Animal experiments

Effect of Dietary Chestnut or Quebracho Tannin Supplementation on Microbial Community and Fatty Acid Profile in the Rumen of Dairy Ewes – Arianna Buccioni – BioMed Research International

Long-Term Treatment with Green Tea Polyphenols Modifies the Gut Microbiome of Female Sprague-Dawley Rats – Jincheng Wang – The Journal of Nutritional Biochemistry

Microbiota-Derived Indole Metabolites Promote Human and Murine Intestinal Homeostasis through Regulation of Interleukin-10 Receptor – Erica E. Alexeev – The Americn Journal of Pathology

Interrelations between the rumen microbiota and production, behavioral, rumen-fermentation, metabolic, and immunological attributes of dairy cows – M. Schären – Journal of Diary Science

Animal microbiome

Disentangling metabolic functions of bacteria in the honey bee gut – Lucie Kešnerová – PLOS One

Plant, root, and soil microbiome

Soil mixture composition alters Arabidopsis susceptibility to Pseudomonas syringae infection – Jana A. Hassan – Plant Direct

Taxonomic structure and function of seed-inhabiting bacterial microbiota from common reed (Phragmites australis) and narrowleaf cattail (Typha angustifolia L.) – Ting Gao – Archives of Microbiology

The soil microbiome — from metagenomics to metaphenomics – Janet K Jansson – Current Opinion in Microbiology

Exometabolomic profiling of bacterial strains cultivated using Arabidopsis root extract as the sole carbon source – Richard Paul Jacoby – Molecular Plant-Microbiome Interactions

A strain of Streptomyces sp. isolated from rhizospheric soil of Crataegus oxycantha producing Nalidixic acid, a synthetic antibiotic – Nidhi Arora – Journal of Applied Microbiology

High microbial diversity promotes soil ecosystem functioning – Pierre-Alain Maron – Applied and Environmental Microbiology

Water and extremophile microbiome 

Apportioning bacterial carbon source utilization in soil using 14C isotope analysis of FISH-targeted bacterial populations sorted by Fluorescence Activated Cell Sorting (FACS): 14C-FISH-FACS – Christos Gougoulias – Environmental Microbiology Reports

Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea – E. J. Fleming – Applied and Environmental Microbiology

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria – Théophile Grébert – PNAS

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning – Zhili He – mBio

Iron and phosphorus deprivation induce sociality in the marine bloom-forming cyanobacterium Trichodesmium – Yael Tzubari – the ISME Journal

Cryptophyta as major bacterivores in freshwater summer plankton – Vesna Grujcic – the ISME Journal

Phages and viruses

The impact of bacteriophages on phyllosphere bacterial abundance and composition – Norma M. Morella – Molecular Ecology

Microbes in the news 

Guts and gory: vampire bats need bacteria to digest blood

Using mutant bacteria to study how changes in membrane proteins affect cell functions